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Kichuk T, Dhamankar S, Malani S, Hofstadter WA, Wegner SA, Cristea IM, Avalos JL. Using MitER for 3D analysis of mitochondrial morphology and ER contacts. Cell Rep Methods 2024; 4:100692. [PMID: 38232737 PMCID: PMC10832265 DOI: 10.1016/j.crmeth.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 09/13/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024]
Abstract
We have developed an open-source workflow that allows for quantitative single-cell analysis of organelle morphology, distribution, and inter-organelle contacts with an emphasis on the analysis of mitochondria and mitochondria-endoplasmic reticulum (mito-ER) contact sites. As the importance of inter-organelle contacts becomes more widely recognized, there is a concomitant increase in demand for tools to analyze subcellular architecture. Here, we describe a workflow we call MitER (pronounced "mightier"), which allows for automated calculation of organelle morphology, distribution, and inter-organelle contacts from 3D renderings by employing the animation software Blender. We then use MitER to quantify the variations in the mito-ER networks of Saccharomyces cerevisiae, revealing significantly more mito-ER contacts within respiring cells compared to fermenting cells. We then demonstrate how this workflow can be applied to mammalian systems and used to monitor mitochondrial dynamics and inter-organelle contact in time-lapse studies.
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Affiliation(s)
- Therese Kichuk
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Satyen Dhamankar
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Saurabh Malani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | | | - Scott A Wegner
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA; High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
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2
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Wang B, Zhao Z, Xiong M, Yan R, Xu K. The endoplasmic reticulum adopts two distinct tubule forms. Proc Natl Acad Sci U S A 2022; 119:e2117559119. [PMID: 35471903 DOI: 10.1073/pnas.2117559119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The endoplasmic reticulum (ER) is one of the most structurally visible and functionally important organelles in the cell. Utilizing superresolution microscopy, we here unveil that in the mammalian cell, the peripheral ER adopts two distinct, well-defined tubule forms of contrasting structures, molecular signatures, and functions, with one of the two curiously being ribbon-like, ultranarrow sheets of fixed widths. With fast multicolor microscopy, we further show how the two tubule forms dynamically interconvert while differentially accommodating proteins in the living cell. The endoplasmic reticulum (ER) is a versatile organelle with diverse functions. Through superresolution microscopy, we show that the peripheral ER in the mammalian cell adopts two distinct forms of tubules. Whereas an ultrathin form, R1, is consistently covered by ER-membrane curvature-promoting proteins, for example, Rtn4 in the native cell, in the second form, R2, Rtn4 and analogs are arranged into two parallel lines at a conserved separation of ∼105 nm over long ranges. The two tubule forms together account for ∼90% of the total tubule length in the cell, with either one being dominant in different cell types. The R1–R2 dichotomy and the final tubule geometry are both coregulated by Rtn4 (and analogs) and the ER sheet–maintaining protein Climp63, which, respectively, define the edge curvature and lumen height of the R2 tubules to generate a ribbon-like structure of well-defined width. Accordingly, the R2 tubule width correlates positively with the Climp63 intraluminal size. The R1 and R2 tubules undergo active remodeling at the second/subsecond timescales as they differently accommodate proteins, with the former effectively excluding ER-luminal proteins and ER-membrane proteins with large intraluminal domains. We thus uncover a dynamic structural dichotomy for ER tubules with intriguing functional implications.
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3
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Avci D, Malchus NS, Heidasch R, Lorenz H, Richter K, Neßling M, Lemberg MK. The intramembrane protease SPP impacts morphology of the endoplasmic reticulum by triggering degradation of morphogenic proteins. J Biol Chem 2018; 294:2786-2800. [PMID: 30578301 DOI: 10.1074/jbc.ra118.005642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/12/2018] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER), as a multifunctional organelle, plays crucial roles in lipid biosynthesis and calcium homeostasis as well as the synthesis and folding of secretory and membrane proteins. Therefore, it is of high importance to maintain ER homeostasis and to adapt ER function and morphology to cellular needs. Here, we show that signal peptide peptidase (SPP) modulates the ER shape through degradation of morphogenic proteins. Elevating SPP activity induces rapid rearrangement of the ER and formation of dynamic ER clusters. Inhibition of SPP activity rescues the phenotype without the need for new protein synthesis, and this rescue depends on a pre-existing pool of proteins in the Golgi. With the help of organelle proteomics, we identified certain membrane proteins to be diminished upon SPP expression and further show that the observed morphology changes depend on SPP-mediated cleavage of ER morphogenic proteins, including the SNARE protein syntaxin-18. Thus, we suggest that SPP-mediated protein abundance control by a regulatory branch of ER-associated degradation (ERAD-R) has a role in shaping the early secretory pathway.
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Affiliation(s)
- Dönem Avci
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Nicole S Malchus
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Ronny Heidasch
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Holger Lorenz
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Karsten Richter
- German Cancer Research Center (DKFZ), Central Unit Electron Microscopy, 69120 Heidelberg, Germany
| | - Michelle Neßling
- German Cancer Research Center (DKFZ), Central Unit Electron Microscopy, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
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Breuss MW, Nguyen A, Song Q, Nguyen T, Stanley V, James KN, Musaev D, Chai G, Wirth SA, Anzenberg P, George RD, Johansen A, Ali S, Zia-Ur-Rehman M, Sultan T, Zaki MS, Gleeson JG. Mutations in LNPK, Encoding the Endoplasmic Reticulum Junction Stabilizer Lunapark, Cause a Recessive Neurodevelopmental Syndrome. Am J Hum Genet 2018; 103:296-304. [PMID: 30032983 PMCID: PMC6080764 DOI: 10.1016/j.ajhg.2018.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/27/2018] [Indexed: 11/16/2022] Open
Abstract
The dynamic shape of the endoplasmic reticulum (ER) is a reflection of its wide variety of critical cell biological functions. Consequently, perturbation of ER-shaping proteins can cause a range of human phenotypes. Here, we describe three affected children (from two consanguineous families) who carry homozygous loss-of-function mutations in LNPK (previously known as KIAA1715); this gene encodes lunapark, which is proposed to serve as a curvature-stabilizing protein within tubular three-way junctions of the ER. All individuals presented with severe psychomotor delay, intellectual disability, hypotonia, epilepsy, and corpus callosum hypoplasia, and two of three showed mild cerebellar hypoplasia and atrophy. Consistent with a proposed role in neurodevelopmental disease, LNPK was expressed during brain development in humans and mice and was present in neurite-like processes in differentiating human neural progenitor cells. Affected cells showed the absence of full-length lunapark, aberrant ER structures, and increased luminal mass density. Together, our results implicate the ER junction stabilizer lunapark in establishing the corpus callosum.
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Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - An Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Qiong Song
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Thai Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Valentina Stanley
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Kiely N James
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Damir Musaev
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Guoliang Chai
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Sara A Wirth
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Paula Anzenberg
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Renee D George
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Anide Johansen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Shaila Ali
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Muhammad Zia-Ur-Rehman
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Joseph G Gleeson
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA.
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5
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Abstract
Three proteins work together to control the shape of the endoplasmic reticulum in animal cells.
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Affiliation(s)
- Craig Blackstone
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - William A Prinz
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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Wang S, Tukachinsky H, Romano FB, Rapoport TA. Cooperation of the ER-shaping proteins atlastin, lunapark, and reticulons to generate a tubular membrane network. eLife 2016; 5. [PMID: 27619977 PMCID: PMC5021524 DOI: 10.7554/elife.18605] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/28/2016] [Indexed: 12/29/2022] Open
Abstract
In higher eukaryotes, the endoplasmic reticulum (ER) contains a network of membrane tubules, which transitions into sheets during mitosis. Network formation involves curvature-stabilizing proteins, including the reticulons (Rtns), as well as the membrane-fusing GTPase atlastin (ATL) and the lunapark protein (Lnp). Here, we have analyzed how these proteins cooperate. ATL is needed to not only form, but also maintain, the ER network. Maintenance requires a balance between ATL and Rtn, as too little ATL activity or too high Rtn4a concentrations cause ER fragmentation. Lnp only affects the abundance of three-way junctions and tubules. We suggest a model in which ATL-mediated fusion counteracts the instability of free tubule ends. ATL tethers and fuses tubules stabilized by the Rtns, and transiently sits in newly formed three-way junctions. Lnp subsequently moves into the junctional sheets and forms oligomers. Lnp is inactivated by mitotic phosphorylation, which contributes to the tubule-to-sheet conversion of the ER.
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Affiliation(s)
- Songyu Wang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Hanna Tukachinsky
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Fabian B Romano
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Tom A Rapoport
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
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Perez AJ, Seyedhosseini M, Deerinck TJ, Bushong EA, Panda S, Tasdizen T, Ellisman MH. A workflow for the automatic segmentation of organelles in electron microscopy image stacks. Front Neuroanat 2014; 8:126. [PMID: 25426032 PMCID: PMC4224098 DOI: 10.3389/fnana.2014.00126] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/19/2014] [Indexed: 11/13/2022] Open
Abstract
Electron microscopy (EM) facilitates analysis of the form, distribution, and functional status of key organelle systems in various pathological processes, including those associated with neurodegenerative disease. Such EM data often provide important new insights into the underlying disease mechanisms. The development of more accurate and efficient methods to quantify changes in subcellular microanatomy has already proven key to understanding the pathogenesis of Parkinson's and Alzheimer's diseases, as well as glaucoma. While our ability to acquire large volumes of 3D EM data is progressing rapidly, more advanced analysis tools are needed to assist in measuring precise three-dimensional morphologies of organelles within data sets that can include hundreds to thousands of whole cells. Although new imaging instrument throughputs can exceed teravoxels of data per day, image segmentation and analysis remain significant bottlenecks to achieving quantitative descriptions of whole cell structural organellomes. Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks. Segmentations are generated using only 2D image information, making the method suitable for anisotropic imaging techniques such as serial block-face scanning electron microscopy (SBEM). Additionally, no assumptions about 3D organelle morphology are made, ensuring the method can be easily expanded to any number of structurally and functionally diverse organelles. Following the presentation of our algorithm, we validate its performance by assessing the segmentation accuracy of different organelle targets in an example SBEM dataset and demonstrate that it can be efficiently parallelized on supercomputing resources, resulting in a dramatic reduction in runtime.
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Affiliation(s)
- Alex J Perez
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA ; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mojtaba Seyedhosseini
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Thomas J Deerinck
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Eric A Bushong
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies La Jolla, CA, USA
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Mark H Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA ; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA ; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
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Abstract
Peroxisomes are the most recently discovered classical organelles, and only lately have their diverse functions been truly recognized. Peroxisomes are highly dynamic structures, changing both morphologically and in number in response to both extracellular and intracellular signals. This metabolic organelle came to prominence due to the many genetic disorders caused by defects in its biogenesis or enzymatic functions. There is now growing evidence that suggests peroxisomes are involved in lipid biosynthesis, innate immunity, redox homeostasis, and metabolite scavenging, among other functions. Therefore, it is important to have available suitable methods and techniques to visualize and quantify peroxisomes in response to various cellular signals. This unit includes a number of protocols that will enable researchers to image, qualify, and quantify peroxisome numbers and morphology-with both steady-state and time-lapse imaging using mammalian cells. The use of photoactivatable fluorescent proteins to detect and measure peroxisome biogenesis is also described. Altogether, the protocols described here will facilitate understanding of the dynamic changes that peroxisomes undergo in response to various cellular signals.
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Affiliation(s)
- Miluska Jauregui
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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Hermann GJ, Thatcher JW, Mills JP, Hales KG, Fuller MT, Nunnari J, Shaw JM. Mitochondrial fusion in yeast requires the transmembrane GTPase Fzo1p. J Cell Biol 1998; 143:359-73. [PMID: 9786948 PMCID: PMC2132826 DOI: 10.1083/jcb.143.2.359] [Citation(s) in RCA: 425] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/1998] [Revised: 08/25/1998] [Indexed: 01/09/2023] Open
Abstract
Membrane fusion is required to establish the morphology and cellular distribution of the mitochondrial compartment. In Drosophila, mutations in the fuzzy onions (fzo) GTPase block a developmentally regulated mitochondrial fusion event during spermatogenesis. Here we report that the yeast orthologue of fuzzy onions, Fzo1p, plays a direct and conserved role in mitochondrial fusion. A conditional fzo1 mutation causes the mitochondrial reticulum to fragment and blocks mitochondrial fusion during yeast mating. Fzo1p is a mitochondrial integral membrane protein with its GTPase domain exposed to the cytoplasm. Point mutations that alter conserved residues in the GTPase domain do not affect Fzo1p localization but disrupt mitochondrial fusion. Suborganellar fractionation suggests that Fzo1p spans the outer and is tightly associated with the inner mitochondrial membrane. This topology may be required to coordinate the behavior of the two mitochondrial membranes during the fusion reaction. We propose that the fuzzy onions family of transmembrane GTPases act as molecular switches to regulate a key step in mitochondrial membrane docking and/or fusion.
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Affiliation(s)
- G J Hermann
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
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