1
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Seifer S, Elbaum M. ClusterAlign: A fiducial tracking and tilt series alignment tool for thick sample tomography. BIOLOGICAL IMAGING 2022; 2:e7. [PMID: 38486831 PMCID: PMC10936405 DOI: 10.1017/s2633903x22000071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 03/17/2024]
Abstract
Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced as fiducial markers, varies strongly through the tilt series. As a result, tedious manual refinement may be required in order to produce a successful alignment. Information from highly tilted views must often be excluded to the detriment of axial resolution in the reconstruction. We introduce here an approach to tilt series alignment based on identification of fiducial particle clusters that transform coherently in rotation, essentially those that lie at similar depth. Clusters are identified by comparison of tilted views with a single untilted reference, rather than with adjacent tilts. The software, called ClusterAlign, proves robust to poor signal to noise ratio and varying visibility of the individual fiducials and is successful in carrying the alignment to the ends of the tilt series where other methods tend to fail. ClusterAlign may be used to generate a list of tracked fiducials, to align a tilt series, or to perform a complete 3D reconstruction. Tools to evaluate alignment error by projection matching are included. Execution involves no manual intervention, and adherence to standard file formats facilitates an interface with other software, particularly IMOD/etomo, tomo3d, and tomoalign.
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Affiliation(s)
- Shahar Seifer
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Elbaum
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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2
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Cheung CY, Huang TT, Chow N, Zhang S, Zhao Y, Chau MP, Chan WC, Wong CCL, Boassa D, Phan S, Ellisman MH, Yates JR, Xu S, Yu Z, Zhang Y, Zhang R, Ng LL, Ko BCB. Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2. J Cell Sci 2022; 135:275560. [PMID: 35635291 PMCID: PMC9377714 DOI: 10.1242/jcs.259280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
NFAT5 is the only known mammalian tonicity-responsive transcription factor with essential role in cellular adaptation to hypertonic stress. It is also implicated in diverse physiological and pathological processes. NFAT5 activity is tightly regulated by extracellular tonicity, but the underlying mechanisms remain elusive. We demonstrated that NFAT5 enters the nucleus via the nuclear pore complex. We found that NFAT5 utilizes a unique nuclear localization signal (NFAT5-NLS) for nuclear import. siRNA screening revealed that only karyopherin β1 (KPNB1), but not karyopherin alpha, is responsible for the nuclear import of NFAT5 via direct interaction with the NFAT5-NLS. Proteomics analysis and siRNA screening further revealed that nuclear export of NFAT5 under hypotonicity is driven by Exportin-T, where the process requires RuvB-Like AAA type ATPase 2 (RUVBL2) as an indispensable chaperone. Our findings have identified an unconventional tonicity-dependent nucleocytoplasmic trafficking pathway for NFAT5, a critical step in orchestrating rapid cellular adaptation to change in extracellular tonicity. These findings offer an opportunity for the development of novel NFAT5 targeting strategies that are potentially useful for the treatment of diseases associated with NFAT5 dysregulation.
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Affiliation(s)
- Chris Y Cheung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ting-Ting Huang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ning Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Shuqi Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mary P Chau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Wing Cheung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Catherine C L Wong
- Center for Precision Medicine Muti-Omics Research, Health Science Center, Peking University, China Clinical Laboratory Department, The Cancer Hospital of the University of Chinese Academy of Sciences, Beijing, China
| | - Daniela Boassa
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, USA.,Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - SongXiao Xu
- The Clinical Laboratory Department, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zicheng Yu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yajing Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Rui Zhang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ling Ling Ng
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ben C B Ko
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
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3
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Ganguly A, Sharma R, Boyer NP, Wernert F, Phan S, Boassa D, Parra L, Das U, Caillol G, Han X, Yates JR, Ellisman MH, Leterrier C, Roy S. Clathrin packets move in slow axonal transport and deliver functional payloads to synapses. Neuron 2021; 109:2884-2901.e7. [PMID: 34534453 DOI: 10.1016/j.neuron.2021.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 06/10/2021] [Accepted: 08/13/2021] [Indexed: 12/25/2022]
Abstract
In non-neuronal cells, clathrin has established roles in endocytosis, with clathrin cages enclosing plasma membrane infoldings, followed by rapid disassembly and reuse of monomers. However, in neurons, clathrin is conveyed in slow axonal transport over days to weeks, and the underlying transport/targeting mechanisms, mobile cargo structures, and even its precise presynaptic localization and physiologic role are unclear. Combining live imaging, photobleaching/conversion, mass spectrometry, electron microscopy, and super-resolution imaging, we found that unlike in dendrites, where clathrin cages rapidly assemble and disassemble, in axons, clathrin and related proteins organize into stable "transport packets" that are unrelated to endocytosis and move intermittently on microtubules, generating an overall slow anterograde flow. At synapses, multiple clathrin packets abut synaptic vesicle (SV) clusters, and clathrin packets also exchange between synaptic boutons in a microtubule-dependent "superpool." Within synaptic boundaries, clathrin is surprisingly dynamic, continuously exchanging between local clathrin assemblies, and its depletion impairs SV recycling. Our data provide a conceptual framework for understanding clathrin trafficking and presynaptic targeting that has functional implications.
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Affiliation(s)
- Archan Ganguly
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Rohan Sharma
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas P Boyer
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Florian Wernert
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Sébastien Phan
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Daniela Boassa
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Leonardo Parra
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Utpal Das
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Ghislaine Caillol
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Xuemei Han
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | | | - Subhojit Roy
- Department of Pathology, 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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4
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Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nat Methods 2021; 18:186-193. [PMID: 33542511 PMCID: PMC7611018 DOI: 10.1038/s41592-020-01054-7] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.
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5
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Han R, Li G, Gao X. Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints. Bioinformatics 2021; 37:107-117. [PMID: 33416867 PMCID: PMC8694346 DOI: 10.1093/bioinformatics/btaa1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/08/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
Motivation Electron tomography (ET) has become an indispensable tool for structural biology studies. In ET, the tilt series alignment and the projection parameter calibration are the key steps toward high-resolution ultrastructure analysis. Usually, fiducial markers are embedded in the sample to aid the alignment. Despite the advances in developing algorithms to find correspondence of fiducial markers from different tilted micrographs, the error rate of the existing methods is still high such that manual correction has to be conducted. In addition, existing algorithms do not work well when the number of fiducial markers is high. Results In this article, we try to completely solve the fiducial marker correspondence problem. We propose to divide the workflow of fiducial marker correspondence into two stages: (i) initial transformation determination, and (ii) local correspondence refinement. In the first stage, we model the transform estimation as a correspondence pair inquiry and verification problem. The local geometric constraints and invariant features are used to reduce the complexity of the problem. In the second stage, we encode the geometric distribution of the fiducial markers by a weighted Gaussian mixture model and introduce drift parameters to correct the effects of beam-induced motion and sample deformation. Comprehensive experiments on real-world datasets demonstrate the robustness, efficiency and effectiveness of the proposed algorithm. Especially, the proposed two-stage algorithm is able to produce an accurate tracking within an average of ⩽ 100 ms per image, even for micrographs with hundreds of fiducial markers, which makes the real-time ET data processing possible. Availability and implementation The code is available at https://github.com/icthrm/auto-tilt-pair. Additionally, the detailed original figures demonstrated in the experiments can be accessed at https://rb.gy/6adtk4. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Renmin Han
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, PR China.,Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Guojun Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, PR China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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6
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Kim KY, Rios LC, Le H, Perez AJ, Phan S, Bushong EA, Deerinck TJ, Liu YH, Ellisman MA, Lev-Ram V, Ju S, Panda SA, Yoon S, Hirayama M, Mure LS, Hatori M, Ellisman MH, Panda S. Synaptic Specializations of Melanopsin-Retinal Ganglion Cells in Multiple Brain Regions Revealed by Genetic Label for Light and Electron Microscopy. Cell Rep 2020; 29:628-644.e6. [PMID: 31618632 DOI: 10.1016/j.celrep.2019.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/01/2019] [Accepted: 09/04/2019] [Indexed: 11/17/2022] Open
Abstract
The form and synaptic fine structure of melanopsin-expressing retinal ganglion cells, also called intrinsically photosensitive retinal ganglion cells (ipRGCs), were determined using a new membrane-targeted version of a genetic probe for correlated light and electron microscopy (CLEM). ipRGCs project to multiple brain regions, and because the method labels the entire neuron, it was possible to analyze nerve terminals in multiple retinorecipient brain regions, including the suprachiasmatic nucleus (SCN), olivary pretectal nucleus (OPN), and subregions of the lateral geniculate. Although ipRGCs provide the only direct retinal input to the OPN and SCN, ipRGC terminal arbors and boutons were found to be remarkably different in each target region. A network of dendro-dendritic chemical synapses (DDCSs) was also revealed in the SCN, with ipRGC axon terminals preferentially synapsing on the DDCS-linked cells. The methods developed to enable this analysis should propel other CLEM studies of long-distance brain circuits at high resolution.
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Affiliation(s)
- Keun-Young Kim
- Department of Neurosciences, University of California at San Diego School of Medicine, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Luis C Rios
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Hiep Le
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alex J Perez
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Sébastien Phan
- Department of Neurosciences, University of California at San Diego School of Medicine, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Eric A Bushong
- Department of Neurosciences, University of California at San Diego School of Medicine, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Thomas J Deerinck
- Department of Neurosciences, University of California at San Diego School of Medicine, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Yu Hsin Liu
- Salk Institute for Biological Studies, La Jolla, CA, USA; Medical Scientist Training Program, University of California at San Diego School of Medicine, La Jolla, CA, USA
| | - Maya A Ellisman
- Biological Sciences Graduate Training Program, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Varda Lev-Ram
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Suyeon Ju
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Sneha A Panda
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - Sanghee Yoon
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | | | - Ludovic S Mure
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Megumi Hatori
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California at San Diego School of Medicine, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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7
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Binns TC, Ayala AX, Grimm JB, Tkachuk AN, Castillon GA, Phan S, Zhang L, Brown TA, Liu Z, Adams SR, Ellisman MH, Koyama M, Lavis LD. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems. Cell Chem Biol 2020; 27:1063-1072.e7. [PMID: 32698018 PMCID: PMC7483975 DOI: 10.1016/j.chembiol.2020.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/04/2020] [Accepted: 06/29/2020] [Indexed: 01/14/2023]
Abstract
Light-mediated chemical reactions are powerful methods for manipulating and interrogating biological systems. Photosensitizers, compounds that generate reactive oxygen species upon excitation with light, can be utilized for numerous biological experiments, but the repertoire of bioavailable photosensitizers is limited. Here, we describe the synthesis, characterization, and utility of two photosensitizers based upon the widely used rhodamine scaffold and demonstrate their efficacy for chromophore-assisted light inactivation, cell ablation in culture and in vivo, and photopolymerization of diaminobenzidine for electron microscopy. These chemical tools will facilitate a broad range of applications spanning from targeted destruction of proteins to high-resolution imaging.
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Affiliation(s)
- Thomas C Binns
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Graduate School, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ariana N Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Guillaume A Castillon
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lixia Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Timothy A Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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8
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Wang Z, Zhang J, Gao W, Liu Z, Wan X, Zhang F. A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography. J Comput Biol 2020; 27:212-222. [PMID: 31794252 DOI: 10.1089/cmb.2019.0287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The "missing wedge" of a single tilt in electron tomography introduces severe artifacts into the reconstructed results. To reduce the "missing wedge" effect, a widely used method is "multiple-tilt reconstruction," which collects projections using multiple axes. However, as the number of tilt series increases, the computing and memory costs also rise. The degree of parallelism is limited by the sample thickness, and a large memory requirement cannot be met by most multicore computers. In our study, we present a new fully distributed multiple-tilt simultaneous iterative reconstruction technique (DM-SIRT). To improve the parallelism of the reconstruction process and reduce the memory requirements of each process, we formulate the multiple-tilt reconstruction as a consensus optimization problem and design a DM-SIRT algorithm. Experiments show that in addition to slightly better resolution, DM-SIRT can obtain a 13.9 × accelerated ratio compared with the full multiple-tilt reconstruction version. It also has a 97% decrease in memory overhead and is 16 times more scalable than the full reconstruction version.
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Affiliation(s)
- Zihao Wang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingrong Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Weifang Gao
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Zhiyong Liu
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Wan
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
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9
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Wesseling JF, Phan S, Bushong EA, Siksou L, Marty S, Pérez-Otaño I, Ellisman M. Sparse force-bearing bridges between neighboring synaptic vesicles. Brain Struct Funct 2019; 224:3263-3276. [PMID: 31667576 PMCID: PMC6875159 DOI: 10.1007/s00429-019-01966-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/05/2019] [Indexed: 12/28/2022]
Abstract
Most vesicles in the interior of synaptic terminals are clustered in clouds close to active zone regions of the plasma membrane where exocytosis occurs. Electron-dense structures, termed bridges, have been reported between a small minority of pairs of neighboring vesicles within the clouds. Synapsin proteins have been implicated previously, but the existence of the bridges as stable structures in vivo has been questioned. Here we use electron tomography to show that the bridges are present but less frequent in synapsin knockouts compared to wildtype. An analysis of distances between neighbors in wildtype tomograms indicated that the bridges are strong enough to resist centrifugal forces likely induced by fixation with aldehydes. The results confirm that the bridges are stable structures and that synapsin proteins are involved in formation or stabilization.
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Affiliation(s)
- John F Wesseling
- Instituto de Neurociencias, CSIC-UMH, San Juan de Alicante, Spain. .,Departmento de Neurociencias (CIMA), Universidad de Navarra, Pamplona, Spain.
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
| | - Léa Siksou
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France.,Global Research and Development, Teva Pharmaceutical Industries Ltd, Netanya, Israel
| | - Serge Marty
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France.,Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | | | - Mark Ellisman
- National Center for Microscopy and Imaging Research and Department of Neuroscience, University of California, San Diego, CA, USA
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10
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Han R, Wan X, Li L, Lawrence A, Yang P, Li Y, Wang S, Sun F, Liu Z, Gao X, Zhang F. AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. Bioinformatics 2019; 35:319-328. [PMID: 30010792 PMCID: PMC6330008 DOI: 10.1093/bioinformatics/bty620] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/11/2018] [Indexed: 11/21/2022] Open
Abstract
Motivation Dual-axis electron tomography is an important 3 D macro-molecular structure reconstruction technology, which can reduce artifacts and suppress the effect of missing wedge. However, the fully automatic data process for dual-axis electron tomography still remains a challenge due to three difficulties: (i) how to track the mass of fiducial markers automatically; (ii) how to integrate the information from the two different tilt series; and (iii) how to cope with the inconsistency between the two different tilt series. Results Here we develop a toolkit for fully automatic alignment of dual-axis electron tomography, with a simultaneous reconstruction procedure. The proposed toolkit and its workflow carries out the following solutions: (i) fully automatic detection and tracking of fiducial markers under large-field datasets; (ii) automatic combination of two different tilt series and global calibration of projection parameters; and (iii) inconsistency correction based on distortion correction parameters and the consequently simultaneous reconstruction. With all of these features, the presented toolkit can achieve accurate alignment and reconstruction simultaneously and conveniently under a single global coordinate system. Availability and implementation The toolkit AuTom-dualx (alignment module dualxmauto and reconstruction module volrec_mltm) are accessible for general application at http://ear.ict.ac.cn, and the key source code is freely available under request. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Renmin Han
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Xiaohua Wan
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lun Li
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Albert Lawrence
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, CA, USA and
| | - Peng Yang
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Yu Li
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Sheng Wang
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Liu
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
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11
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Two Pathways for the Activity-Dependent Growth and Differentiation of Synaptic Boutons in Drosophila. eNeuro 2019; 6:ENEURO.0060-19.2019. [PMID: 31387877 PMCID: PMC6709223 DOI: 10.1523/eneuro.0060-19.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 11/21/2022] Open
Abstract
Synapse formation can be promoted by intense activity. At the Drosophila larval neuromuscular junction (NMJ), new synaptic boutons can grow acutely in response to patterned stimulation. We combined confocal imaging with electron microscopy and tomography to investigate the initial stages of growth and differentiation of new presynaptic boutons at the Drosophila NMJ. We found that the new boutons can form rapidly in intact larva in response to intense crawling activity, and we observed two different patterns of bouton formation and maturation. The first pathway involves the growth of filopodia followed by a formation of boutons that are initially devoid of synaptic vesicles (SVs) but filled with filamentous matrix. The second pathway involves rapid budding of synaptic boutons packed with SVs, and these more mature boutons are sometimes capable of exocytosis/endocytosis. We demonstrated that intense activity predominantly promotes the second pathway, i.e., budding of more mature boutons filled with SVs. We also showed that this pathway depends on synapsin (Syn), a neuronal protein which reversibly associates with SVs and mediates their clustering via a protein kinase A (PKA)-dependent mechanism. Finally, we took advantage of the temperature-sensitive mutant sei to demonstrate that seizure activity can promote very rapid budding of new boutons filled with SVs, and this process occurs at scale of minutes. Altogether, these results demonstrate that intense activity acutely and selectively promotes rapid budding of new relatively mature presynaptic boutons filled with SVs, and that this process is regulated via a PKA/Syn-dependent pathway.
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12
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Consideration of sample motion in cryo-tomography based on alignment residual interpolation. J Struct Biol 2019; 205:1-6. [PMID: 30690142 DOI: 10.1016/j.jsb.2019.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/24/2022]
Abstract
Recently, it has been shown that the resolution in cryo-tomography could be improved by considering the sample motion in tilt-series alignment and reconstruction, where a set of quadratic polynomials were used to model this motion. One requirement of this polynomial method is the optimization of a large number of parameters, which may limit its practical applicability. In this work, we propose an alternative method for modeling the sample motion. Starting from the standard fiducial-based tilt-series alignment, the method uses the alignment residual as local estimates of the sample motion at the 3D fiducial positions. Then, a scattered data interpolation technique characterized by its smoothness and a closed-form solution is applied to model the sample motion. The motion model is then integrated in the tomographic reconstruction. The new method improves the tomogram quality similar to the polynomial one, with the important advantage that the determination of the motion model is greatly simplified, thereby overcoming one of the major limitations of the polynomial model. Therefore, the new method is expected to make the beam-induced motion correction methodology more accessible to the cryoET community.
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13
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Dynamic Tomographic Reconstruction of Deforming Volumes. MATERIALS 2018; 11:ma11081395. [PMID: 30096947 PMCID: PMC6119884 DOI: 10.3390/ma11081395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/20/2022]
Abstract
The motion of a sample while being scanned in a tomograph prevents its proper volume reconstruction. In the present study, a procedure is proposed that aims at estimating both the kinematics of the sample and its standard 3D imaging from a standard acquisition protocol (no more projection than for a rigid specimen). The proposed procedure is a staggered two-step algorithm where the volume is first reconstructed using a “Dynamic Reconstruction” technique, a variant of Algebraic Reconstruction Technique (ART) compensating for a “frozen” determination of the motion, followed by a Projection-based Digital Volume Correlation (P-DVC) algorithm that estimates the space/time displacement field, with a “frozen” microstructure and shape of the sample. Additionally, this procedure is combined with a multi-scale approach that is essential for a proper separation between motion and microstructure. A proof-of-concept of the validity and performance of this approach is proposed based on two virtual examples. The studied cases involve a small number of projections, large strains, up to 25%, and noise.
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14
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Han R, Zhang F, Gao X. A fast fiducial marker tracking model for fully automatic alignment in electron tomography. Bioinformatics 2018; 34:853-863. [PMID: 29069299 PMCID: PMC6030832 DOI: 10.1093/bioinformatics/btx653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 11/25/2022] Open
Abstract
Motivation Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner. Results In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers. Availability and implementation The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the '-t' option. Contact xin.gao@kaust.edu.sa. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Renmin Han
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
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15
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Fernandez JJ, Li S, Bharat TAM, Agard DA. Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion. J Struct Biol 2018; 202:200-209. [PMID: 29410148 PMCID: PMC5949096 DOI: 10.1016/j.jsb.2018.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/18/2022]
Abstract
Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET.
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Affiliation(s)
| | - Sam Li
- Dept. Biochemistry and Biophysics, University of California, San Francisco, USA
| | - Tanmay A M Bharat
- MRC Laboratory of Molecular Biology, Francis Crick Avenue Cambridge CB2 0QH, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David A Agard
- Dept. Biochemistry and Biophysics, University of California, San Francisco, USA
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16
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Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 2018; 357:357/6349/eaag0025. [PMID: 28751582 DOI: 10.1126/science.aag0025] [Citation(s) in RCA: 505] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 01/11/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022]
Abstract
The chromatin structure of DNA determines genome compaction and activity in the nucleus. On the basis of in vitro structures and electron microscopy (EM) studies, the hierarchical model is that 11-nanometer DNA-nucleosome polymers fold into 30- and subsequently into 120- and 300- to 700-nanometer fibers and mitotic chromosomes. To visualize chromatin in situ, we identified a fluorescent dye that stains DNA with an osmiophilic polymer and selectively enhances its contrast in EM. Using ChromEMT (ChromEM tomography), we reveal the ultrastructure and three-dimensional (3D) organization of individual chromatin polymers, megabase domains, and mitotic chromosomes. We show that chromatin is a disordered 5- to 24-nanometer-diameter curvilinear chain that is packed together at different 3D concentration distributions in interphase and mitosis. Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.
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Affiliation(s)
- Horng D Ou
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrea Thor
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.,Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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17
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Gürsoy D, Hong YP, He K, Hujsak K, Yoo S, Chen S, Li Y, Ge M, Miller LM, Chu YS, De Andrade V, He K, Cossairt O, Katsaggelos AK, Jacobsen C. Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection. Sci Rep 2017; 7:11818. [PMID: 28924196 PMCID: PMC5603591 DOI: 10.1038/s41598-017-12141-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/22/2017] [Indexed: 11/16/2022] Open
Abstract
As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the same error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.
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Affiliation(s)
- Doğa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA.
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
| | - Young P Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Kuan He
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Karl Hujsak
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Seunghwan Yoo
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA
| | - Yue Li
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Mingyuan Ge
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11967, USA
| | - Lisa M Miller
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11967, USA
| | - Yong S Chu
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11967, USA
| | - Vincent De Andrade
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA
| | - Kai He
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Oliver Cossairt
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Aggelos K Katsaggelos
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, 60439, USA
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
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18
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A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6482567. [PMID: 29312997 PMCID: PMC5623807 DOI: 10.1155/2017/6482567] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/09/2017] [Indexed: 11/18/2022]
Abstract
One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).
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19
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Sastri M, Darshi M, Mackey M, Ramachandra R, Ju S, Phan S, Adams S, Stein K, Douglas CR, Kim JJ, Ellisman MH, Taylor SS, Perkins GA. Sub-mitochondrial localization of the genetic-tagged mitochondrial intermembrane space-bridging components Mic19, Mic60 and Sam50. J Cell Sci 2017; 130:3248-3260. [PMID: 28808085 DOI: 10.1242/jcs.201400] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 08/02/2017] [Indexed: 01/14/2023] Open
Abstract
Each mitochondrial compartment contains varying protein compositions that underlie a diversity of localized functions. Insights into the localization of mitochondrial intermembrane space-bridging (MIB) components will have an impact on our understanding of mitochondrial architecture, dynamics and function. By using the novel visualizable genetic tags miniSOG and APEX2 in cultured mouse cardiac and human astrocyte cell lines and performing electron tomography, we have mapped at nanoscale resolution three key MIB components, Mic19, Mic60 and Sam50 (also known as CHCHD3, IMMT and SAMM50, respectively), in the environment of structural landmarks such as cristae and crista junctions (CJs). Tagged Mic19 and Mic60 were located at CJs, distributed in a network pattern along the mitochondrial periphery and also enriched inside cristae. We discovered an association of Mic19 with cytochrome c oxidase subunit IV. It was also found that tagged Sam50 is not uniformly distributed in the outer mitochondrial membrane and appears to incompletely overlap with Mic19- or Mic60-positive domains, most notably at the CJs.
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Affiliation(s)
- Mira Sastri
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Manjula Darshi
- Howard Hughes Medical Institute, University of California, San Diego, CA 92093, USA
| | - Mason Mackey
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Saeyeon Ju
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Stephen Adams
- Department of Pharmacology, University of California, San Diego, CA 92093, USA
| | - Kathryn Stein
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Christopher R Douglas
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Jiwan John Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA.,Howard Hughes Medical Institute, University of California, San Diego, CA 92093, USA.,Department of Pharmacology, University of California, San Diego, CA 92093, USA
| | - Guy A Perkins
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
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20
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AuTom: A novel automatic platform for electron tomography reconstruction. J Struct Biol 2017; 199:196-208. [PMID: 28756247 DOI: 10.1016/j.jsb.2017.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 12/31/2022]
Abstract
We have developed a software package towards automatic electron tomography (ET): Automatic Tomography (AuTom). The presented package has the following characteristics: accurate alignment modules for marker-free datasets containing substantial biological structures; fully automatic alignment modules for datasets with fiducial markers; wide coverage of reconstruction methods including a new iterative method based on the compressed-sensing theory that suppresses the "missing wedge" effect; and multi-platform acceleration solutions that support faster iterative algebraic reconstruction. AuTom aims to achieve fully automatic alignment and reconstruction for electron tomography and has already been successful for a variety of datasets. AuTom also offers user-friendly interface and auxiliary designs for file management and workflow management, in which fiducial marker-based datasets and marker-free datasets are addressed with totally different subprocesses. With all of these features, AuTom can serve as a convenient and effective tool for processing in electron tomography.
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21
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Yin X, Kidd GJ, Ohno N, Perkins GA, Ellisman MH, Bastian C, Brunet S, Baltan S, Trapp BD. Proteolipid protein-deficient myelin promotes axonal mitochondrial dysfunction via altered metabolic coupling. J Cell Biol 2017; 215:531-542. [PMID: 27872255 PMCID: PMC5119941 DOI: 10.1083/jcb.201607099] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/01/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
The authors show that central nervous system myelin lacking proteolipid protein (PLP) induces mitochondrial dysfunction, including altered motility, degeneration, and ectopic smooth endoplasmic reticulum interactions, leading to axonal structural defects and degeneration. Mutated PLP occurs in hereditary spastic paraplegia, and these cellular effects provide potential insight into the pathology of the disease. Hereditary spastic paraplegia (HSP) is a neurological syndrome characterized by degeneration of central nervous system (CNS) axons. Mutated HSP proteins include myelin proteolipid protein (PLP) and axon-enriched proteins involved in mitochondrial function, smooth endoplasmic reticulum (SER) structure, and microtubule (MT) stability/function. We characterized axonal mitochondria, SER, and MTs in rodent optic nerves where PLP is replaced by the peripheral nerve myelin protein, P0 (P0-CNS mice). Mitochondrial pathology and degeneration were prominent in juxtaparanodal axoplasm at 1 mo of age. In wild-type (WT) optic nerve axons, 25% of mitochondria–SER associations occurred on extensions of the mitochondrial outer membrane. Mitochondria–SER associations were reduced by 86% in 1-mo-old P0-CNS juxtaparanodal axoplasm. 1-mo-old P0-CNS optic nerves were more sensitive to oxygen-glucose deprivation and contained less adenosine triphosphate (ATP) than WT nerves. MT pathology and paranodal axonal ovoids were prominent at 6 mo. These data support juxtaparanodal mitochondrial degeneration, reduced mitochondria–SER associations, and reduced ATP production as causes of axonal ovoid formation and axonal degeneration.
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Affiliation(s)
- Xinghua Yin
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Grahame J Kidd
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Nobuhiko Ohno
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Guy A Perkins
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093
| | - Chinthasagar Bastian
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Sylvain Brunet
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Selva Baltan
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Bruce D Trapp
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
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22
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Wan X, Katchalski T, Churas C, Ghosh S, Phan S, Lawrence A, Hao Y, Zhou Z, Chen R, Chen Y, Zhang F, Ellisman MH. Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods. J Struct Biol 2017; 198:103-115. [PMID: 28392451 DOI: 10.1016/j.jsb.2017.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/22/2016] [Accepted: 04/03/2017] [Indexed: 11/16/2022]
Abstract
Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography.
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Affiliation(s)
- Xiaohua Wan
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Tsvi Katchalski
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Christopher Churas
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Sreya Ghosh
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Albert Lawrence
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA.
| | - Yu Hao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Ziying Zhou
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Beijing Institute of Technology, Beijing, China
| | - Ruijuan Chen
- School of Electronic and Information Engineering, Tianjin Polytechnic University, Tianjin, China; National Center for Microscopy and Imaging Research, University of California, San Diego, USA
| | - Yu Chen
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Fa Zhang
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, USA; Departments of Neurosciences and Bioengineering, University of California, San Diego, USA
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23
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Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Nat Biotechnol 2016; 34:774-80. [PMID: 27240195 PMCID: PMC4942342 DOI: 10.1038/nbt.3563] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 12/26/2022]
Abstract
Intercellular protein-protein interactions (PPIs) enable communication between cells in diverse biological processes, including cell proliferation, immune responses, infection, and synaptic transmission, but they are challenging to visualize because existing techniques have insufficient sensitivity and/or specificity. Here we report a split horseradish peroxidase (sHRP) as a sensitive and specific tool for the detection of intercellular PPIs. The two sHRP fragments, engineered through screening of 17 cut sites in HRP followed by directed evolution, reconstitute into an active form when driven together by an intercellular PPI, producing bright fluorescence or contrast for electron microscopy. Fusing the sHRP fragments to the proteins neurexin (NRX) and neuroligin (NLG), which bind each other across the synaptic cleft, enabled sensitive visualization of synapses between specific sets of neurons, including two classes of synapses in the mouse visual system. sHRP should be widely applicable to studying mechanisms of communication between a variety of cell types.
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Affiliation(s)
- Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Masahito Yamagata
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Carolyn G Kwa
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
- Department of Neurosciences, University of California at San Diego, La Jolla, San Diego, California, USA
- Salk Institute for Biological Studies, La Jolla, San Diego, California, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Phan S, Boassa D, Nguyen P, Wan X, Lanman J, Lawrence A, Ellisman MH. 3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography. ACTA ACUST UNITED AC 2016; 2:8. [PMID: 27547706 PMCID: PMC4972035 DOI: 10.1186/s40679-016-0021-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022]
Abstract
Transmission electron microscopy allows the collection of multiple views of specimens and their computerized three-dimensional reconstruction and analysis with electron tomography. Here we describe development of methods for automated multi-tilt data acquisition, tilt-series processing, and alignment which allow assembly of electron tomographic data from a greater number of tilt series, yielding enhanced data quality and increasing contrast associated with weakly stained structures. This scheme facilitates visualization of nanometer scale details of fine structure in volumes taken from plastic-embedded samples of biological specimens in all dimensions. As heavy metal-contrasted plastic-embedded samples are less sensitive to the overall dose rather than the electron dose rate, an optimal resampling of the reconstruction space can be achieved by accumulating lower dose electron micrographs of the same area over a wider range of specimen orientations. The computerized multiple tilt series collection scheme is implemented together with automated advanced procedures making collection, image alignment, and processing of multi-tilt tomography data a seamless process. We demonstrate high-quality reconstructions from samples of well-described biological structures. These include the giant Mimivirus and clathrin-coated vesicles, imaged in situ in their normal intracellular contexts. Examples are provided from samples of cultured cells prepared by high-pressure freezing and freeze-substitution as well as by chemical fixation before epoxy resin embedding.
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Affiliation(s)
- Sébastien Phan
- National Center For Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA
| | - Daniela Boassa
- National Center For Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA
| | - Phuong Nguyen
- National Center For Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA
| | - Xiaohua Wan
- National Center For Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA
| | - Jason Lanman
- Departments of Neurosciences and Bioengineering, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA.,Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054 USA
| | - Albert Lawrence
- National Center For Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA
| | - Mark H Ellisman
- National Center For Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA.,Departments of Neurosciences and Bioengineering, University of California, 9500 Gilman Drive La Jolla, San Diego, CA 92093-0608, USA.,Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054 USA
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Han R, Wang L, Liu Z, Sun F, Zhang F. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. J Struct Biol 2015; 192:403-417. [DOI: 10.1016/j.jsb.2015.09.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/25/2015] [Accepted: 09/30/2015] [Indexed: 12/20/2022]
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26
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Nuclear pore complex remodeling by p75(NTR) cleavage controls TGF-β signaling and astrocyte functions. Nat Neurosci 2015; 18:1077-80. [PMID: 26120963 PMCID: PMC4878404 DOI: 10.1038/nn.4054] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 06/04/2015] [Indexed: 12/22/2022]
Abstract
Astrocytes modulate neuronal activity and inhibit regeneration. We show that cleaved p75 neurotrophin receptor (p75(NTR)) is a component of the nuclear pore complex (NPC) required for glial scar formation and reduced gamma oscillations in mice via regulation of transforming growth factor (TGF)-β signaling. Cleaved p75(NTR) interacts with nucleoporins to promote Smad2 nucleocytoplasmic shuttling. Thus, NPC remodeling by regulated intramembrane cleavage of p75(NTR) controls astrocyte-neuronal communication in response to profibrotic factors.
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27
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Perkins GA, Jackson DR, Spirou GA. Resolving presynaptic structure by electron tomography. Synapse 2015; 69:268-82. [PMID: 25683026 DOI: 10.1002/syn.21813] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/07/2015] [Accepted: 02/11/2015] [Indexed: 01/09/2023]
Abstract
A key goal in neurobiology is to generate a theoretical framework that merges structural, physiological, and molecular explanations of brain function. These categories of explanation do not advance in synchrony; advances in one category define new experiments in other categories. For example, the synapse was defined physiologically and biochemically before it was visualized using electron microscopy. Indeed, the original descriptions of synapses in the 1950s were lent credence by the presence of spherical vesicles in presynaptic terminals that were considered to be the substrate for quantal neurotransmission. In the last few decades, our understanding of synaptic function has again been driven by physiological and molecular techniques. The key molecular players for synaptic vesicle structure, mobility and fusion were identified and applications of the patch clamp technique permitted physiological estimation of neurotransmitter release and receptor properties. These advances demand higher resolution structural images of synapses. During the 1990s a second renaissance in cell biology driven by EM was fueled by improved techniques for electron tomography (ET) with the ability to compute virtual images with nm resolution between image planes. Over the last 15 years, ET has been applied to the presynaptic terminal with special attention to the active zone and organelles of the nerve terminal. In this review, we first summarize the technical improvements that have led to a resurgence in utilization of ET and then we summarize new insights gained by the application of ET to reveal the high-resolution structure of the nerve terminal.
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Affiliation(s)
- Guy A Perkins
- National Center for Microscopy and Imaging Research, University of California, San Diego, San Diego, California, 92092-0608
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Zhang F, Zhang J, Lawrence A, Ren F, Wang X, Liu Z, Wan X. BSIRT: a block-iterative SIRT parallel algorithm using curvilinear projection model. IEEE Trans Nanobioscience 2015; 14:229-36. [PMID: 25680211 DOI: 10.1109/tnb.2015.2393377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Large-field high-resolution electron tomography enables visualizing detailed mechanisms under global structure. As field enlarges, the distortions of reconstruction and processing time become more critical. Using the curvilinear projection model can improve the quality of large-field ET reconstruction, but its computational complexity further exacerbates the processing time. Moreover, there is no parallel strategy on GPU for iterative reconstruction method with curvilinear projection. Here we propose a new Block-iterative SIRT parallel algorithm with the curvilinear projection model (BSIRT) for large-field ET reconstruction, to improve the quality of reconstruction and accelerate the reconstruction process. We also develop some key techniques, including block-iterative method with the curvilinear projection, a scope-based data decomposition method and a page-based data transfer scheme to implement the parallelization of BSIRT on GPU platform. Experimental results show that BSIRT can improve the reconstruction quality as well as the speed of the reconstruction process.
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29
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Boassa D, Nguyen P, Hu J, Ellisman MH, Sosinsky GE. Pannexin2 oligomers localize in the membranes of endosomal vesicles in mammalian cells while Pannexin1 channels traffic to the plasma membrane. Front Cell Neurosci 2015; 8:468. [PMID: 25698922 PMCID: PMC4313697 DOI: 10.3389/fncel.2014.00468] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/27/2014] [Indexed: 12/13/2022] Open
Abstract
Pannexin2 (Panx2) is the largest of three members of the pannexin proteins. Pannexins are topologically related to connexins and innexins, but serve different functional roles than forming gap junctions. We previously showed that pannexins form oligomeric channels but unlike connexins and innexins, they form only single membrane channels. High levels of Panx2 mRNA and protein in the Central Nervous System (CNS) have been documented. Whereas Pannexin1 (Panx1) is fairly ubiquitous and Pannexin3 (Panx3) is found in skin and connective tissue, both are fully glycosylated, traffic to the plasma membrane and have functions correlated with extracellular ATP release. Here, we describe trafficking and subcellular localizations of exogenous Panx2 and Panx1 protein expression in MDCK, HeLa, and HEK 293T cells as well as endogenous Panx1 and Panx2 patterns in the CNS. Panx2 was found in intracellular localizations, was partially N-glycosylated, and localizations were non-overlapping with Panx1. Confocal images of hippocampal sections immunolabeled for the astrocytic protein GFAP, Panx1 and Panx2 demonstrated that the two isoforms, Panx1 and Panx2, localized at different subcellular compartments in both astrocytes and neurons. Using recombinant fusions of Panx2 with appended genetic tags developed for correlated light and electron microscopy and then expressed in different cell lines, we determined that Panx2 is localized in the membrane of intracellular vesicles and not in the endoplasmic reticulum as initially indicated by calnexin colocalization experiments. Dual immunofluorescence imaging with protein markers for specific vesicle compartments showed that Panx2 vesicles are early endosomal in origin. In electron tomographic volumes, cross-sections of these vesicles displayed fine structural details and close proximity to actin filaments. Thus, pannexins expressed at different subcellular compartments likely exert distinct functional roles, particularly in the nervous system.
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Affiliation(s)
- Daniela Boassa
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
| | - Phuong Nguyen
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
| | - Junru Hu
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA ; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Gina E Sosinsky
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, 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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Kageyama Y, Hoshijima M, Seo K, Bedja D, Sysa-Shah P, Andrabi SA, Chen W, Höke A, Dawson VL, Dawson TM, Gabrielson K, Kass DA, Iijima M, Sesaki H. Parkin-independent mitophagy requires Drp1 and maintains the integrity of mammalian heart and brain. EMBO J 2014; 33:2798-813. [PMID: 25349190 PMCID: PMC4282557 DOI: 10.15252/embj.201488658] [Citation(s) in RCA: 335] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/18/2014] [Accepted: 09/19/2014] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial dynamics and mitophagy have been linked to cardiovascular and neurodegenerative diseases. Here, we demonstrate that the mitochondrial division dynamin Drp1 and the Parkinson's disease-associated E3 ubiquitin ligase parkin synergistically maintain the integrity of mitochondrial structure and function in mouse heart and brain. Mice lacking cardiac Drp1 exhibited lethal heart defects. In Drp1KO cardiomyocytes, mitochondria increased their connectivity, accumulated ubiquitinated proteins, and decreased their respiration. In contrast to the current views of the role of parkin in ubiquitination of mitochondrial proteins, mitochondrial ubiquitination was independent of parkin in Drp1KO hearts, and simultaneous loss of Drp1 and parkin worsened cardiac defects. Drp1 and parkin also play synergistic roles in neuronal mitochondrial homeostasis and survival. Mitochondrial degradation was further decreased by combination of Drp1 and parkin deficiency, compared with their single loss. Thus, the physiological importance of parkin in mitochondrial homeostasis is revealed in the absence of mitochondrial division in mammals.
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Affiliation(s)
- Yusuke Kageyama
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Masahiko Hoshijima
- Center for Research in Biological Systems and Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kinya Seo
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Djahida Bedja
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Polina Sysa-Shah
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shaida A Andrabi
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Weiran Chen
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ahmet Höke
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Kathleen Gabrielson
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Kass
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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31
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Hou Y, Crossman DJ, Rajagopal V, Baddeley D, Jayasinghe I, Soeller C. Super-resolution fluorescence imaging to study cardiac biophysics: α-actinin distribution and Z-disk topologies in optically thick cardiac tissue slices. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:328-39. [PMID: 25042577 DOI: 10.1016/j.pbiomolbio.2014.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
A major motivation for the use of super-resolution imaging methods in the investigation of cardiac biophysics has been the insight from biophysical considerations and detailed mathematical modeling that the spatial structure and protein organisation at the scale of nanometres can have enormous implications for calcium signalling in cardiac muscle. We illustrate the use of dSTORM based super-resolution in optically thick (∼10 μm) tissue slices of rat ventricular tissue to visualize proteins at the cardiac Z-disk and compare those images with confocal (diffraction-limited) as well as electron microscopy (EM) data which still provides a benchmark in terms of resolution. α-actinin is an abundant protein target that effectively defines the Z-disk in striated muscle and provides a reference structure for other proteins at the Z-line and the transverse tubules. Using super-resolution imaging α-actinin labelling provides very detailed outlines of the contractile machinery which we have used to study the properties of Z-disks and the distribution of α-actinin itself. We determined the local diameters of the myo-fibrillar and non-myofibrillar space using α-actinin labelling. Comparison between confocal and super-resolution based myofibrillar masks suggested that super-resolution data was able to segment myofibrils accurately while confocal approaches were not always able to distinguish neighbouring myofibrillar bundles which resulted in overestimated diameters. The increased resolution of super-resolution methods provides qualitatively new information to improve our understanding of cardiac biophysics. Nevertheless, conventional diffraction-limited imaging still has an important role to play which we illustrate with correlative confocal and super-resolution data.
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Affiliation(s)
- Yufeng Hou
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - David J Crossman
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Vijay Rajagopal
- Dept. of Electrical and Electronic Engineering, University of Melbourne, Australia
| | - David Baddeley
- Department of Physiology, University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University, New Haven, USA
| | | | - Christian Soeller
- Department of Physiology, University of Auckland, Auckland, New Zealand; Biomedical Physics, University of Exeter, UK.
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32
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Davis CHO, Kim KY, Bushong EA, Mills EA, Boassa D, Shih T, Kinebuchi M, Phan S, Zhou Y, Bihlmeyer NA, Nguyen JV, Jin Y, Ellisman MH, Marsh-Armstrong N. Transcellular degradation of axonal mitochondria. Proc Natl Acad Sci U S A 2014; 111:9633-8. [PMID: 24979790 PMCID: PMC4084443 DOI: 10.1073/pnas.1404651111] [Citation(s) in RCA: 442] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
It is generally accepted that healthy cells degrade their own mitochondria. Here, we report that retinal ganglion cell axons of WT mice shed mitochondria at the optic nerve head (ONH), and that these mitochondria are internalized and degraded by adjacent astrocytes. EM demonstrates that mitochondria are shed through formation of large protrusions that originate from otherwise healthy axons. A virally introduced tandem fluorophore protein reporter of acidified mitochondria reveals that acidified axonal mitochondria originating from the retinal ganglion cell are associated with lysosomes within columns of astrocytes in the ONH. According to this reporter, a greater proportion of retinal ganglion cell mitochondria are degraded at the ONH than in the ganglion cell soma. Consistently, analyses of degrading DNA reveal extensive mtDNA degradation within the optic nerve astrocytes, some of which comes from retinal ganglion cell axons. Together, these results demonstrate that surprisingly large proportions of retinal ganglion cell axonal mitochondria are normally degraded by the astrocytes of the ONH. This transcellular degradation of mitochondria, or transmitophagy, likely occurs elsewhere in the CNS, because structurally similar accumulations of degrading mitochondria are also found along neurites in superficial layers of the cerebral cortex. Thus, the general assumption that neurons or other cells necessarily degrade their own mitochondria should be reconsidered.
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Affiliation(s)
- Chung-ha O Davis
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Keun-Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Elizabeth A Mills
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Tiffany Shih
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Mira Kinebuchi
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Yi Zhou
- Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Nathan A Bihlmeyer
- Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Judy V Nguyen
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Yunju Jin
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Nicholas Marsh-Armstrong
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
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33
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Han R, Zhang F, Wan X, Fernández JJ, Sun F, Liu Z. A marker-free automatic alignment method based on scale-invariant features. J Struct Biol 2014; 186:167-80. [DOI: 10.1016/j.jsb.2014.02.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 11/30/2022]
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Abstract
Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility.
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Kittelmann M, Hegermann J, Goncharov A, Taru H, Ellisman MH, Richmond JE, Jin Y, Eimer S. Liprin-α/SYD-2 determines the size of dense projections in presynaptic active zones in C. elegans. J Cell Biol 2013; 203:849-63. [PMID: 24322429 PMCID: PMC3857474 DOI: 10.1083/jcb.201302022] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 11/06/2013] [Indexed: 01/23/2023] Open
Abstract
Synaptic vesicle (SV) release is spatially and temporally regulated by a network of proteins that form the presynaptic active zone (AZ). The hallmark of most AZs is an electron-dense projection (DP) surrounded by SVs. Despite their importance for our understanding of triggered SV release, high-resolution analyses of DP structures are limited. Using electron microscopy, we show that DPs at Caenorhabditis elegans neuromuscular junctions (NMJs) were highly structured, composed of building units forming bays in which SVs are docked to the AZ membrane. Furthermore, larger ribbonlike DPs that were multimers of the NMJ building unit are found at synapses between inter- and motoneurons. We also demonstrate that DP size is determined by the activity of the AZ protein SYD-2/Liprin-α. Whereas loss of syd-2 function led to smaller DPs, syd-2 gain-of-function mutants displayed larger ribbonlike DPs through increased recruitment of ELKS-1/ELKS. Therefore, our data suggest that a main role of SYD-2/Liprin-α in synaptogenesis is to regulate the polymerization of DPs.
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Affiliation(s)
- Maike Kittelmann
- European Neuroscience Institute, 37077 Göttingen, Germany
- Cellular Neurobiology, Schwann-Schleiden-Centre for Molecular Cell Biology, 37077 Göttingen, Germany
| | - Jan Hegermann
- European Neuroscience Institute, 37077 Göttingen, Germany
- Center for Molecular Physiology of the Brain, 37073 Göttingen, Germany
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
| | - Alexandr Goncharov
- Howard Hughes Medical Institute, Division of Biological Sciences; and Center for Research on Biological Systems, National Center for Microscopy and Imaging Research and Department of Neurosciences; University of California, San Diego, La Jolla, CA 92093
| | - Hidenori Taru
- Howard Hughes Medical Institute, Division of Biological Sciences; and Center for Research on Biological Systems, National Center for Microscopy and Imaging Research and Department of Neurosciences; University of California, San Diego, La Jolla, CA 92093
- Laboratory of Neuronal Cell Biology, Graduate School of Pharmaceutical Sciences and Creative Research Institute, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Mark H. Ellisman
- Howard Hughes Medical Institute, Division of Biological Sciences; and Center for Research on Biological Systems, National Center for Microscopy and Imaging Research and Department of Neurosciences; University of California, San Diego, La Jolla, CA 92093
| | - Janet E. Richmond
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Yishi Jin
- Howard Hughes Medical Institute, Division of Biological Sciences; and Center for Research on Biological Systems, National Center for Microscopy and Imaging Research and Department of Neurosciences; University of California, San Diego, La Jolla, CA 92093
| | - Stefan Eimer
- European Neuroscience Institute, 37077 Göttingen, Germany
- Center for Molecular Physiology of the Brain, 37073 Göttingen, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79108 Freiburg, Germany
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36
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Burette AC, Lesperance T, Crum J, Martone M, Volkmann N, Ellisman MH, Weinberg RJ. Electron tomographic analysis of synaptic ultrastructure. J Comp Neurol 2013; 520:2697-711. [PMID: 22684938 DOI: 10.1002/cne.23067] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synaptic function depends on interactions among sets of proteins that assemble into complex supramolecular machines. Molecular biology, electrophysiology, and live-cell imaging studies have provided tantalizing glimpses into the inner workings of the synapse, but fundamental questions remain regarding the functional organization of these "nano-machines." Electron tomography reveals the internal structure of synapses in three dimensions with exceptional spatial resolution. Here we report results from an electron tomographic study of axospinous synapses in neocortex and hippocampus of the adult rat, based on aldehyde-fixed material stabilized with tannic acid in lieu of postfixation with osmium tetroxide. Our results provide a new window into the structural basis of excitatory synaptic processing in the mammalian brain.
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Affiliation(s)
- Alain C Burette
- Department of Cell & Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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37
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Mapping the subcellular distribution of α-synuclein in neurons using genetically encoded probes for correlated light and electron microscopy: implications for Parkinson's disease pathogenesis. J Neurosci 2013; 33:2605-15. [PMID: 23392688 DOI: 10.1523/jneurosci.2898-12.2013] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Modifications to the gene encoding human α-synuclein have been linked to the development of Parkinson's disease. The highly conserved structure of α-synuclein suggests a functional interaction with membranes, and several lines of evidence point to a role in vesicle-related processes within nerve terminals. Using recombinant fusions of human α-synuclein, including new genetic tags developed for correlated light microscopy and electron microscopy (the tetracysteine-biarsenical labeling system or the new fluorescent protein for electron microscopy, MiniSOG), we determined the distribution of α-synuclein when overexpressed in primary neurons at supramolecular and cellular scales in three dimensions (3D). We observed specific association of α-synuclein with a large and otherwise poorly characterized membranous organelle system of the presynaptic terminal, as well as with smaller vesicular structures within these boutons. Furthermore, α-synuclein was localized to multiple elements of the protein degradation pathway, including multivesicular bodies in the axons and lysosomes within neuronal cell bodies. Examination of synapses in brains of transgenic mice overexpressing human α-synuclein revealed alterations of the presynaptic endomembrane systems similar to our findings in cell culture. Three-dimensional electron tomographic analysis of enlarged presynaptic terminals in several brain areas revealed that these terminals were filled with membrane-bounded organelles, including tubulovesicular structures similar to what we observed in vitro. We propose that α-synuclein overexpression is associated with hypertrophy of membrane systems of the presynaptic terminal previously shown to have a role in vesicle recycling. Our data support the conclusion that α-synuclein is involved in processes associated with the sorting, channeling, packaging, and transport of synaptic material destined for degradation.
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38
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Loss of OPA1 disturbs cellular calcium homeostasis and sensitizes for excitotoxicity. Cell Death Differ 2012; 20:353-65. [PMID: 23138851 DOI: 10.1038/cdd.2012.128] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Optic atrophy 1 (OPA1) mutations cause dominant optic atrophy (DOA) with retinal ganglion cell (RGC) and optic nerve degeneration. The mechanism for the selective degeneration of RGCs in DOA remains elusive. To address the mechanism, we reduced OPA1 protein expression in cell lines and RGCs by RNA interference. OPA1 loss results in mitochondrial fragmentation, deficiency in oxidative phosphorylation, decreased ATP levels, decreased mitochondrial Ca(2+) retention capacity, reduced mtDNA copy numbers, and sensitization to apoptotic insults. We demonstrate profound cristae depletion and loss of crista junctions in OPA1 knockdown cells, whereas the remaining crista junctions preserve their normal size. OPA1-depleted cells exhibit decreased agonist-evoked mitochondrial Ca(2+) transients and corresponding reduction of NAD(+) to NADH, but the impairment in NADH oxidation leads to an overall more reduced mitochondrial NADH pool. Although in our model OPA1 loss in RGCs has no apparent impact on mitochondrial morphology, it decreases buffering of cytosolic Ca(2+) and sensitizes RGCs to excitotoxic injury. Exposure to glutamate triggers delayed calcium deregulation (DCD), often in a reversible manner, indicating partial resistance of RGCs to this injury. However, when OPA1 is depleted, DCD becomes irreversible. Thus, our data show that whereas OPA1 is required for mitochondrial fusion, maintenance of crista morphology and oxidative phosphorylation, loss of OPA1 also results in defective Ca(2+) homeostasis.
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39
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Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat Biotechnol 2012; 30:1143-8. [PMID: 23086203 PMCID: PMC3699407 DOI: 10.1038/nbt.2375] [Citation(s) in RCA: 491] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/29/2012] [Indexed: 11/09/2022]
Abstract
Electron microscopy (EM) is the standard method for imaging cellular structures with nanometer resolution, but existing genetic tags are inactive in most cellular compartments or require light and can be difficult to use. Here we report the development of 'APEX', a genetically encodable EM tag that is active in all cellular compartments and does not require light. APEX is a monomeric 28-kDa peroxidase that withstands strong EM fixation to give excellent ultrastructural preservation. We demonstrate the utility of APEX for high-resolution EM imaging of a variety of mammalian organelles and specific proteins using a simple and robust labeling procedure. We also fused APEX to the N or C terminus of the mitochondrial calcium uniporter (MCU), a recently identified channel whose topology is disputed. These fusions give EM contrast exclusively in the mitochondrial matrix, suggesting that both the N and C termini of MCU face the matrix. Because APEX staining is not dependent on light activation, APEX should make EM imaging of any cellular protein straightforward, regardless of the size or thickness of the specimen.
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Affiliation(s)
- Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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40
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Ou HD, Kwiatkowski W, Deerinck TJ, Noske A, Blain KY, Land HS, Soria C, Powers CJ, May AP, Shu X, Tsien RY, Fitzpatrick JA, Long JA, Ellisman MH, Choe S, O’Shea CC. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell 2012; 151:304-19. [PMID: 23063122 PMCID: PMC3681303 DOI: 10.1016/j.cell.2012.08.035] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/10/2012] [Accepted: 08/16/2012] [Indexed: 12/21/2022]
Abstract
Evolution of minimal DNA tumor virus' genomes has selected for small viral oncoproteins that hijack critical cellular protein interaction networks. The structural basis for the multiple and dominant functions of adenovirus oncoproteins has remained elusive. E4-ORF3 forms a nuclear polymer and simultaneously inactivates p53, PML, TRIM24, and MRE11/RAD50/NBS1 (MRN) tumor suppressors. We identify oligomerization mutants and solve the crystal structure of E4-ORF3. E4-ORF3 forms a dimer with a central β core, and its structure is unrelated to known polymers or oncogenes. E4-ORF3 dimer units coassemble through reciprocal and nonreciprocal exchanges of their C-terminal tails. This results in linear and branched oligomer chains that further assemble in variable arrangements to form a polymer network that partitions the nuclear volume. E4-ORF3 assembly creates avidity-driven interactions with PML and an emergent MRN binding interface. This reveals an elegant structural solution whereby a small protein forms a multivalent matrix that traps disparate tumor suppressors.
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Affiliation(s)
- Horng D. Ou
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Witek Kwiatkowski
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas J. Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrew Noske
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Katie Y. Blain
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hannah S. Land
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Conrado Soria
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Colin J. Powers
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew P. May
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, 555 Mission Bay Blvd South, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Roger Y. Tsien
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Departments of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - James A.J. Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeff A. Long
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Senyon Choe
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Clodagh C. O’Shea
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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41
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Fernandez JJ. Computational methods for electron tomography. Micron 2012; 43:1010-30. [DOI: 10.1016/j.micron.2012.05.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/08/2012] [Accepted: 05/08/2012] [Indexed: 01/13/2023]
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42
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Ultrastructural modifications in the mitochondria of hypoxia-adapted Drosophila melanogaster. PLoS One 2012; 7:e45344. [PMID: 23028948 PMCID: PMC3446896 DOI: 10.1371/journal.pone.0045344] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 08/21/2012] [Indexed: 01/05/2023] Open
Abstract
Chronic hypoxia (CH) occurs under certain physiological or pathological conditions, including in people who reside at high altitude or suffer chronic cardiovascular or pulmonary diseases. As mitochondria are the predominant oxygen-consuming organelles to generate ATP through oxidative phosphorylation in cells, their responses, through structural or molecular modifications, to limited oxygen supply play an important role in the overall functional adaptation to hypoxia. Here, we report the adaptive mitochondrial ultrastructural modifications and the functional impacts in a recently generated hypoxia-adapted Drosophila melanogaster strain that survives severe, otherwise lethal, hypoxic conditions. Using electron tomography, we discovered increased mitochondrial volume density and cristae abundance, yet also cristae fragmentation and a unique honeycomb-like structure in the mitochondria of hypoxia-adapted flies. The homeostatic levels of adenylate and energy charge were similar between hypoxia-adapted and naïve control flies and the hypoxia-adapted flies remained active under severe hypoxia as quantified by negative geotaxis behavior. The equilibrium ATP level was lower in hypoxia-adapted flies than those of the naïve controls tested under severe hypoxia that inhibited the motion of control flies. Our results suggest that the structural rearrangement in the mitochondria of hypoxia-adapted flies may be an important adaptive mechanism that plays a critical role in preserving adenylate homeostasis and metabolism as well as muscle function under chronic hypoxic conditions.
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43
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Phan S, Lawrence A, Molina T, Lanman J, Berlanga M, Terada M, Kulungowski A, Obayashi J, Ellisman M. TxBR montage reconstruction for large field electron tomography. J Struct Biol 2012; 180:154-64. [PMID: 22749959 DOI: 10.1016/j.jsb.2012.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/05/2012] [Accepted: 06/12/2012] [Indexed: 11/18/2022]
Abstract
Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a consequence, are rather difficult to generate directly. Various techniques have been developed towards generating those views, from increasing the sensor array size to implementing serial sectioning and montaging. Datasets and reconstructions obtained by the latter techniques generate multiple three-dimensional (3D) reconstructions, that need to be combined together to provide all the multiscale information. In this work, we show how to implement montages within TxBR, a tomographic reconstruction software package. This work involves some new application of mathematical concepts related to volume preserving transformations and issues of gauge ambiguity, which are essential problems arising from the nature of the observation in an electron microscope. The purpose of TxBR is to handle those issues as generally as possible in order to correct for most distortions in the 3D reconstructions and allow for a seamless recombination of ET montages.
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Affiliation(s)
- Sébastien Phan
- National Center For Microscopy and Imaging Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA
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44
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Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:49-90. [PMID: 22297510 DOI: 10.1007/978-1-4614-0980-9_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The past few decades have seen tremendous advances in single-particle electron -cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures "in situ". Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.
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45
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Astakhov V, Bandrowski A, Gupta A, Kulungowski AW, Grethe JS, Bouwer J, Molina T, Rowley V, Penticoff S, Terada M, Wong W, Hakozaki H, Kwon O, Martone ME, Ellisman M. Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics. ACTA ACUST UNITED AC 2012; 9:1595-1603. [PMID: 28479932 PMCID: PMC5415345 DOI: 10.1016/j.procs.2012.04.175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report on progress of employing the Kepler workflow engine to prototype “end-to-end” application integration workflows that concern data coming from microscopes deployed at the National Center for Microscopy Imaging Research (NCMIR). This system is built upon the mature code base of the Cell Centered Database (CCDB) and integrated rule-oriented data system (IRODS) for distributed storage. It provides integration with external projects such as the Whole Brain Catalog (WBC) and Neuroscience Information Framework (NIF), which benefit from NCMIR data. We also report on specific workflows which spawn from main workflows and perform data fusion and orchestration of Web services specific for the NIF project. This “Brain data flow” presents a user with categorized information about sources that have information on various brain regions.
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Affiliation(s)
- V Astakhov
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - A Bandrowski
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - A Gupta
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - A W Kulungowski
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - J S Grethe
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - J Bouwer
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - T Molina
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - V Rowley
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - S Penticoff
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - M Terada
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - W Wong
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - H Hakozaki
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - O Kwon
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - M E Martone
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - M Ellisman
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
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46
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Abstract
The electron microscope has contributed deep insights into biological structure since its invention nearly 80 years ago. Advances in instrumentation and methodology in recent decades have now enabled electron tomography to become the highest resolution three-dimensional (3D) imaging technique available for unique objects such as cells. Cells can be imaged either plastic-embedded or frozen-hydrated. Then the series of projection images are aligned and back-projected to generate a 3D reconstruction or 'tomogram'. Here, we review how electron tomography has begun to reveal the molecular organization of cells and how the existing and upcoming technologies promise even greater insights into structural cell biology.
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47
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Kett LR, Boassa D, Ho CCY, Rideout HJ, Hu J, Terada M, Ellisman M, Dauer WT. LRRK2 Parkinson disease mutations enhance its microtubule association. Hum Mol Genet 2011; 21:890-9. [PMID: 22080837 DOI: 10.1093/hmg/ddr526] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dominant missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic causes of Parkinson disease (PD) and genome-wide association studies identify LRRK2 sequence variants as risk factors for sporadic PD. Intact kinase function appears critical for the toxicity of LRRK2 PD mutants, yet our understanding of how LRRK2 causes neurodegeneration remains limited. We find that most LRRK2 PD mutants abnormally enhance LRRK2 oligomerization, causing it to form filamentous structures in transfections of cell lines or primary neuronal cultures. Strikingly, ultrastructural analyses, including immuno-electron microscopy and electron microscopic tomography, demonstrate that these filaments consist of LRRK2 recruited onto part of the cellular microtubule network in a well-ordered, periodic fashion. Like LRRK2-related neurodegeneration, microtubule association requires intact kinase function and the WD40 domain, potentially linking microtubule binding and neurodegeneration. Our observations identify a novel effect of LRRK2 PD mutations and highlight a potential role for microtubules in the pathogenesis of LRRK2-related neurodegeneration.
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Affiliation(s)
- Lauren R Kett
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
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48
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Berlanga ML, Price DL, Phung BS, Giuly R, Terada M, Yamada N, Cyr M, Caron MG, Laakso A, Martone ME, Ellisman MH. Multiscale imaging characterization of dopamine transporter knockout mice reveals regional alterations in spine density of medium spiny neurons. Brain Res 2011; 1390:41-9. [PMID: 21439946 DOI: 10.1016/j.brainres.2011.03.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 03/16/2011] [Accepted: 03/17/2011] [Indexed: 11/26/2022]
Abstract
The dopamine transporter knockout (DAT KO) mouse is a model of chronic hyperdopaminergia used to study a wide range of neuropsychiatric disorders such as schizophrenia, attention deficit hyperactivity disorder (ADHD), drug abuse, depression, and Parkinson's disease (PD). Early studies characterizing this mouse model revealed a subtle, but significant, decrease in the anterior striatal volume of DAT KO mice accompanied by a decrease in neuronal cell body numbers (Cyr et al., 2005). The present studies were conducted to examine medium spiny neuron (MSN) morphology by extending these earlier reports to include multiscale imaging studies using correlated light microscopy (LM) and electron microscopy (EM) techniques. Specifically, we set out to determine if chronic hyperdopaminergia results in quantifiable or qualitative changes in DAT KO mouse MSNs relative to wild-type (WT) littermates. Using Neurolucida Explorer's morphometric analysis, we measured spine density, dendritic length and synapse number at ages that correspond with the previously reported changes in striatal volume and progressive cell loss. Light microscopic analysis using Neurolucida tracings of photoconverted striatal MSNs revealed a highly localized loss of dendritic spines on the proximal portion of the dendrite (30 μm from the soma) in the DAT KO group. Next, thick sections containing MSN dendritic segments located at a distance of 20-60 μm from the cell soma, a region of the dendrite where spine density is reported to be the highest, were analyzed using electron microscope tomography (EMT). Because of the resolution limits of LM, the EM analysis was an extra measure taken to assure that our analysis included nearly all spines. Spine density measurements collected from the EMT data revealed only a modest decrease in the DAT KO group (n=3 mice) compared to age-matched WT controls (n=3 mice), a trend that supports the LM findings. Finally, a synaptic quantification using unbiased stereology did not detect a difference between DAT KO mice (n=6 mice) and WT controls (n=7 mice) at the EM level, supporting the focal nature of the early synaptic loss. These findings suggest that DAT KO mice have MSNs with highly localized spine loss and not an overall morphologically distinct cell shape. The characterization of morphological changes in DAT KO mice may provide information about the neural substrates underlying altered behaviors in these mice, with relevance for human neurological disorders thought to involve altered dopaminergic homeostasis. Results from this study also indicate the difficulty in correlating structural changes across scales, as the results on fine structure revealed thus far are subtle and non-uniform across striatal MSNs. The complexities associated with multiscale studies are driving the development of shared online informatics resources by gaining access to data where it is being analyzed.
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Affiliation(s)
- M L Berlanga
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093-0608, USA.
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49
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Darshi M, Mendiola VL, Mackey MR, Murphy AN, Koller A, Perkins GA, Ellisman MH, Taylor SS. ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function. J Biol Chem 2010; 286:2918-32. [PMID: 21081504 PMCID: PMC3024787 DOI: 10.1074/jbc.m110.171975] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial inner membrane (IM) serves as the site for ATP production by hosting the oxidative phosphorylation complex machinery most notably on the crista membranes. Disruption of the crista structure has been implicated in a variety of cardiovascular and neurodegenerative diseases. Here, we characterize ChChd3, a previously identified PKA substrate of unknown function (Schauble, S., King, C. C., Darshi, M., Koller, A., Shah, K., and Taylor, S. S. (2007) J. Biol. Chem. 282, 14952-14959), and show that it is essential for maintaining crista integrity and mitochondrial function. In the mitochondria, ChChd3 is a peripheral protein of the IM facing the intermembrane space. RNAi knockdown of ChChd3 in HeLa cells resulted in fragmented mitochondria, reduced OPA1 protein levels and impaired fusion, and clustering of the mitochondria around the nucleus along with reduced growth rate. Both the oxygen consumption and glycolytic rates were severely restricted. Ultrastructural analysis of these cells revealed aberrant mitochondrial IM structures with fragmented and tubular cristae or loss of cristae, and reduced crista membrane. Additionally, the crista junction opening diameter was reduced to 50% suggesting remodeling of cristae in the absence of ChChd3. Analysis of the ChChd3-binding proteins revealed that ChChd3 interacts with the IM proteins mitofilin and OPA1, which regulate crista morphology, and the outer membrane protein Sam50, which regulates import and assembly of β-barrel proteins on the outer membrane. Knockdown of ChChd3 led to almost complete loss of both mitofilin and Sam50 proteins and alterations in several mitochondrial proteins, suggesting that ChChd3 is a scaffolding protein that stabilizes protein complexes involved in maintaining crista architecture and protein import and is thus essential for maintaining mitochondrial structure and function.
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Affiliation(s)
- Manjula Darshi
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0654, USA
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50
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Kim KY, Ju WK, Hegedus B, Gutmann DH, Ellisman MH. Ultrastructural characterization of the optic pathway in a mouse model of neurofibromatosis-1 optic glioma. Neuroscience 2010; 170:178-88. [PMID: 20600672 DOI: 10.1016/j.neuroscience.2010.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 12/30/2022]
Abstract
The purpose of this study was to investigate the progression of changes in retinal ganglion cells and optic nerve glia in neurofibromatosis-1 (NF1) genetically-engineered mice with optic glioma. Optic glioma tumors were generated in Nf1+/- mice lacking Nf1 expression in GFAP+ cells (astrocytes). Standard immunohistochemistry methods were employed to identify astrocytes (GFAP, S100beta), proliferating progenitor cells (sox2, nestin), microglia (Iba1), endothelial cells (CD31) and retinal ganglion cell (RGC) axons (Neurofilament 68k) in Nf1+/-, Nf1(GFAP)CKO (wild-type mice with Nf1 loss in glial cells), and Nf1+/-(GFAP)CKO (Nf1+/- mice with Nf1 loss in glial cells) mice. Ultrastructural changes in the optic chiasm and nerve were assessed by electron microscopy (EM). RGC were counted in whole retina preparations using high-resolution, mosaic confocal microscopy following their delineation by retrograde FluoroGold labeling. We found that only Nf1+/-(GFAP)CKO mice exhibited gross pre-chiasmatic optic nerve and chiasm enlargements containing aggregated GFAP+/nestin+ and S100beta+/sox2+ cells (neoplastic glia) as well as increased numbers of blood vessels and microglia. Optic gliomas in Nf1+/-(GFAP)CKO mice contained axon fiber irregularities and multilamellar bodies of degenerated myelin. EM and EM tomographic analyses showed increased glial disorganization, disoriented axonal projections, profiles of degenerating myelin and structural alterations at nodes of Ranvier. Lastly, we found reduced RGC numbers in Nf1+/-(GFAP)CKO mice, supporting a model in which the combination of optic nerve Nf1 heterozygosity and glial cell Nf1 loss results in disrupted axonal-glial relationships, subsequently culminating in the degeneration of optic nerve axons and loss of their parent RGC neurons.
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Affiliation(s)
- K Y Kim
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research and Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA 92037, USA
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