1
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Are extraordinary nucleosome structures more ordinary than we thought? Chromosoma 2023:10.1007/s00412-023-00791-w. [PMID: 36917245 DOI: 10.1007/s00412-023-00791-w] [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: 01/23/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/16/2023]
Abstract
The nucleosome is a DNA-protein assembly that is the basic unit of chromatin. A nucleosome can adopt various structures. In the canonical nucleosome structure, 145-147 bp of DNA is wrapped around a histone heterooctamer. The strong histone-DNA interactions cause the DNA to be inaccessible for nuclear processes such as transcription. Therefore, the canonical nucleosome structure has to be altered into different, non-canonical structures to increase DNA accessibility. While it is recognised that non-canonical structures do exist, these structures are not well understood. In this review, we discuss both the evidence for various non-canonical nucleosome structures in the nucleus and the factors that are believed to induce these structures. The wide range of non-canonical structures is likely to regulate the amount of accessible DNA, and thus have important nuclear functions.
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2
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Jiang W, Wagner J, Du W, Plitzko J, Baumeister W, Beck F, Guo Q. A transformation clustering algorithm and its application in polyribosomes structural profiling. Nucleic Acids Res 2022; 50:9001-9011. [PMID: 35811088 PMCID: PMC9458451 DOI: 10.1093/nar/gkac547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 12/26/2022] Open
Abstract
Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. Beyond such analyses of individual macromolecules, the study of their interactions with functionally related neighbors in crowded cellular habitats, i.e. ‘molecular sociology’, is of fundamental importance in biology. Here we present a NEighboring Molecule TOpology Clustering (NEMO-TOC) algorithm. We optimized this algorithm for the detection and profiling of polyribosomes, which play both constitutive and regulatory roles in gene expression. Our results suggest a model where polysomes are formed by connecting multiple nonstochastic blocks, in which translation is likely synchronized.
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Affiliation(s)
- Wenhong Jiang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University , Beijing 100871, China
| | - Jonathan Wagner
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University , Beijing 100871, China
| | - Juergen Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Florian Beck
- CryoEM Technology, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University , Beijing 100871, China
- Changping Laboratory , Beijing, China
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3
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Foster HE, Ventura Santos C, Carter AP. A cryo-ET survey of microtubules and intracellular compartments in mammalian axons. J Cell Biol 2022; 221:e202103154. [PMID: 34878519 PMCID: PMC7612188 DOI: 10.1083/jcb.202103154] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
The neuronal axon is packed with cytoskeletal filaments, membranes, and organelles, many of which move between the cell body and axon tip. Here, we used cryo-electron tomography to survey the internal components of mammalian sensory axons. We determined the polarity of the axonal microtubules (MTs) by combining subtomogram classification and visual inspection, finding MT plus and minus ends are structurally similar. Subtomogram averaging of globular densities in the MT lumen suggests they have a defined structure, which is surprising given they likely contain the disordered protein MAP6. We found the endoplasmic reticulum in axons is tethered to MTs through multiple short linkers. We surveyed membrane-bound cargos and describe unexpected internal features such as granules and broken membranes. In addition, we detected proteinaceous compartments, including numerous virus-like capsid particles. Our observations outline novel features of axonal cargos and MTs, providing a platform for identification of their constituents.
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4
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Entropy-regularized deconvolution of cellular cryotransmission electron tomograms. Proc Natl Acad Sci U S A 2021; 118:2108738118. [PMID: 34876518 PMCID: PMC8685678 DOI: 10.1073/pnas.2108738118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/01/2022] Open
Abstract
Cellular cryo-electron tomography suffers from severely compromised Z resolution due to the missing wedges of information not collected during the acquisition of tilt series. This paper shows that application of entropy-regularized deconvolution to transmission electron tomography substantially fills in this missing information, allowing for improved Z resolution and better interpretation of cellular structures. Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).
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5
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Narayan V, McMahon M, O'Brien JJ, McAllister F, Buffenstein R. Insights into the Molecular Basis of Genome Stability and Pristine Proteostasis in Naked Mole-Rats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1319:287-314. [PMID: 34424521 DOI: 10.1007/978-3-030-65943-1_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The naked mole-rat (Heterocephalus glaber) is the longest-lived rodent, with a maximal reported lifespan of 37 years. In addition to its long lifespan - which is much greater than predicted based on its small body size (longevity quotient of ~4.2) - naked mole-rats are also remarkably healthy well into old age. This is reflected in a striking resistance to tumorigenesis and minimal declines in cardiovascular, neurological and reproductive function in older animals. Over the past two decades, researchers have been investigating the molecular mechanisms regulating the extended life- and health- span of this animal, and since the sequencing and assembly of the naked mole-rat genome in 2011, progress has been rapid. Here, we summarize findings from published studies exploring the unique molecular biology of the naked mole-rat, with a focus on mechanisms and pathways contributing to genome stability and maintenance of proteostasis during aging. We also present new data from our laboratory relevant to the topic and discuss our findings in the context of the published literature.
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Affiliation(s)
| | - Mary McMahon
- Calico Life Sciences, LLC, South San Francisco, CA, USA
| | | | | | - Rochelle Buffenstein
- Calico Life Sciences, LLC, South San Francisco, CA, USA. .,Department of Pharmacology, University of Texas Health at San Antonio, San Antonio, TX, USA.
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6
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Reboud-Ravaux M. [The proteasome - structural aspects and inhibitors: a second life for a validated drug target]. Biol Aujourdhui 2021; 215:1-23. [PMID: 34397372 DOI: 10.1051/jbio/2021005] [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] [Received: 04/06/2021] [Indexed: 02/06/2023]
Abstract
The proteasome is the central component of the adaptable ubiquitin proteasome system (UPS) discovered in the 1980's. It sustains protein homeostasis (proteostasis) under a large variety of physiological and pathological conditions. Its dysregulation has been often associated to various human diseases. Its potential regulation by modulators has emerged as promising avenue to develop treatments of various pathologies. The FDA approval in 2003 of the proteasome inhibitor bortezomib to treat multiple myeloma, then mantle lymphoma in 2006, has considerably increased the clinical interest of proteasome inhibition. Second-generation proteasome inhibitors (carfilzomib and ixazomib) have been approved to overcome bortezomib resistance and improved toxicity profile and route of administration. Selective inhibition of immunoproteasome is a promising approach towards the development of immunomodulatory drugs. The design of these drugs relies greatly on the elucidation of high-resolution structures of the targeted proteasomes. The ATPase-dependent 26S proteasome (2.4 MDa) consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of catalytic sites. In recent years, due to technical advances especially in atomic cryo-electron microscopy, significant progress has been made in the understanding of 26S proteasome structure and its dynamics. Stepwise conformational changes of the 19S particle induced by ATP hydrolysis lead to substrate translocation, 20S pore opening and processive protein degradation by the 20S proteolytic subunits (2β1, 2β2 and 2β5). A large variety of structurally different inhibitors, both natural products or synthetic compounds targeting immuno- and constitutive proteasomes, has been discovered. The latest advances in this drug discovery are presented. Knowledge about structures, inhibition mechanism and detailed biological regulations of proteasomes can guide strategies for the development of next-generation inhibitors to treat human diseases, especially cancers, immune disorders and pathogen infections. Proteasome activators are also potentially applicable to the reduction of proteotoxic stresses in neurodegeneration and aging.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
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7
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Bäuerlein FJB, Baumeister W. Towards Visual Proteomics at High Resolution. J Mol Biol 2021; 433:167187. [PMID: 34384780 DOI: 10.1016/j.jmb.2021.167187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.
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Affiliation(s)
- Felix J B Bäuerlein
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany; Georg-August-University, Institute for Neuropathology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany.
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8
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Floyd BM, Drew K, Marcotte EM. Systematic Identification of Protein Phosphorylation-Mediated Interactions. J Proteome Res 2021; 20:1359-1370. [PMID: 33476154 DOI: 10.1021/acs.jproteome.0c00750] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein phosphorylation is a key regulatory mechanism involved in nearly every eukaryotic cellular process. Increasingly sensitive mass spectrometry approaches have identified hundreds of thousands of phosphorylation sites, but the functions of a vast majority of these sites remain unknown, with fewer than 5% of sites currently assigned a function. To increase our understanding of functional protein phosphorylation we developed an approach (phospho-DIFFRAC) for identifying the phosphorylation-dependence of protein assemblies in a systematic manner. A combination of nonspecific protein phosphatase treatment, size-exclusion chromatography, and mass spectrometry allowed us to identify changes in protein interactions after the removal of phosphate modifications. With this approach we were able to identify 316 proteins involved in phosphorylation-sensitive interactions. We recovered known phosphorylation-dependent interactors such as the FACT complex and spliceosome, as well as identified novel interactions such as the tripeptidyl peptidase TPP2 and the supraspliceosome component ZRANB2. More generally, we find phosphorylation-dependent interactors to be strongly enriched for RNA-binding proteins, providing new insight into the role of phosphorylation in RNA binding. By searching directly for phosphorylated amino acid residues in mass spectrometry data, we identified the likely regulatory phosphosites on ZRANB2 and FACT complex subunit SSRP1. This study provides both a method and resource for obtaining a better understanding of the role of phosphorylation in native macromolecular assemblies. All mass spectrometry data are available through PRIDE (accession #PXD021422).
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Affiliation(s)
- Brendan M Floyd
- Department of Molecular Biosciences Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kevin Drew
- Department of Molecular Biosciences Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edward M Marcotte
- Department of Molecular Biosciences Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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9
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Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
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Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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10
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Greene ER, Dong KC, Martin A. Understanding the 26S proteasome molecular machine from a structural and conformational dynamics perspective. Curr Opin Struct Biol 2019; 61:33-41. [PMID: 31783300 DOI: 10.1016/j.sbi.2019.10.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022]
Abstract
The 26S proteasome is the essential compartmental protease in eukaryotic cells required for the ubiquitin-dependent clearance of damaged polypeptides and obsolete regulatory proteins. Recently, a combination of high-resolution structural, biochemical, and biophysical studies has provided crucial new insights into the mechanisms of this fascinating molecular machine. A multitude of new cryo-electron microscopy structures provided snapshots of the proteasome during ATP-hydrolysis-driven substrate translocation, and detailed biochemical studies revealed the timing of individual degradation steps, elucidating the mechanisms for substrate selection and the commitment to degradation through conformational transitions. It was uncovered how ubiquitin removal from substrates is mechanically coupled to degradation, and cryo-electron tomography studies gave a glimpse of active proteasomes inside the cell, their subcellular localization, and interactions with protein aggregates. Here, we summarize these advances in our mechanistic understanding of the proteasome, with a particular focus on how its structural features and conformational transitions enable the multi-step degradation process.
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Affiliation(s)
- Eric R Greene
- Department of Molecular Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ken C Dong
- Department of Molecular Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Andreas Martin
- Department of Molecular Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA.
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11
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Tomkinson B. Tripeptidyl-peptidase II: Update on an oldie that still counts. Biochimie 2019; 166:27-37. [DOI: 10.1016/j.biochi.2019.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022]
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12
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Zhang P. Advances in cryo-electron tomography and subtomogram averaging and classification. Curr Opin Struct Biol 2019; 58:249-258. [PMID: 31280905 PMCID: PMC6863431 DOI: 10.1016/j.sbi.2019.05.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022]
Abstract
Cryo-electron tomography (cryoET) can provide 3D reconstructions, or tomograms, of pleomorphic objects such as organelles or cells in their close-to-native states. Subtomograms that contain repetitive structures can be further extracted and subjected to averaging and classification to improve resolution, and this process has become an emerging structural biology method referred to as cryoET subtomogram averaging and classification (cryoSTAC). Recent technical advances in cryoSTAC have had a profound impact on many fields in biology. Here, I review recent exciting work on several macromolecular assemblies demonstrating the power of cryoSTAC for in situ structure analysis and discuss challenges and future directions.
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Affiliation(s)
- Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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13
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Wang HW, Fan X. Challenges and opportunities in cryo-EM with phase plate. Curr Opin Struct Biol 2019; 58:175-182. [PMID: 31374473 DOI: 10.1016/j.sbi.2019.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
Not long after the invention of transmission electron microscope (TEM), phase plate was proposed as a novel electron-optical apparatus at the back-focal plane of the objective lens to modulate the magnified specimen images with enhanced contrast, especially in cryo-electron microscopy (cryo-EM) application of biological specimens. In the past two decades, novel phase plates of different kinds were designed and fabricated for cryo-EM application. Some of them such as the Volta phase plate have already been proved very useful in single particle cryo-EM and cryo-electron tomography (cryo-ET) analysis. In this review, we discuss the current progress, challenges and opportunities of cryo-EM with phase plate.
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Affiliation(s)
- Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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14
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15
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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16
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Englmeier R, Förster F. Cryo-electron tomography for the structural study of mitochondrial translation. Tissue Cell 2018; 57:129-138. [PMID: 30197222 DOI: 10.1016/j.tice.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/29/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Cryo-electron tomography (cryo-ET) enables the three-dimensional (3D) structural characterization of macromolecular complexes in their physiological environment. Thus, cryo-ET is uniquely suited to study the structural basis of biomolecular processes that are extremely difficult or even impossible to reconstitute using purified components. Translation of mitochondrial genes, which occurs in the secluded interior of mitochondria, falls into this category. Here, we describe the principles of cryo-ET in the context of mitochondrial translation and outline recent developments and challenges of the method. The 3D image of a frozen-hydrated biological sample is computed from its 2D projections, which are acquired using a transmission electron microscope. In conjunction with automated detection of different copies of the molecule of interest and averaging of the corresponding subtomograms, cryo-ET enables macromolecular structure determination in the native environment (i.e. in situ) at sub-nanometer resolution. The preservation of the native environment furthermore allows the extraction of contextual information about the molecules, including the location of specific molecules with respect to membranes, their relative positioning and the spatial organization with respect to other types of macromolecules. Recent preparative developments extend the field of application of cryo-ET from isolated organelles to cultured eukaryotic cells and even tissue, making the traditional borders between molecular and cellular structural biology disappear.
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Affiliation(s)
- Robert Englmeier
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.
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17
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Expanding horizons of cryo-tomography to larger volumes. Curr Opin Microbiol 2018; 43:155-161. [DOI: 10.1016/j.mib.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/18/2022]
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18
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Mishra R, Upadhyay A, Prajapati VK, Mishra A. Proteasome-mediated proteostasis: Novel medicinal and pharmacological strategies for diseases. Med Res Rev 2018; 38:1916-1973. [DOI: 10.1002/med.21502] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/13/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Ribhav Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Vijay Kumar Prajapati
- Department of Biochemistry; School of Life Sciences; Central University of Rajasthan; Rajasthan India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
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19
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Anderson KL, Page C, Swift MF, Hanein D, Volkmann N. Marker-free method for accurate alignment between correlated light, cryo-light, and electron cryo-microscopy data using sample support features. J Struct Biol 2018; 201:46-51. [PMID: 29113849 PMCID: PMC5748349 DOI: 10.1016/j.jsb.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/30/2022]
Abstract
Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film. We find that the accuracy of this method, as judged by prediction errors of the hole center coordinates, is better than 100 nm.
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Affiliation(s)
- Karen L Anderson
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Christopher Page
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Mark F Swift
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Dorit Hanein
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Niels Volkmann
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA.
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Wagner J, Schaffer M, Fernández-Busnadiego R. Cryo-electron tomography-the cell biology that came in from the cold. FEBS Lett 2017; 591:2520-2533. [PMID: 28726246 DOI: 10.1002/1873-3468.12757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/26/2017] [Accepted: 07/14/2017] [Indexed: 12/27/2022]
Abstract
Cryo-electron tomography (cryo-ET) provides high-resolution 3D views into cells pristinely preserved by vitrification. Recent technical advances such as direct electron detectors, the Volta phase plate and cryo-focused ion beam milling have dramatically pushed image quality and expanded the range of cryo-ET applications. Cryo-ET not only allows mapping the positions and interactions of macromolecules within their intact cellular context, but can also reveal their in situ structure at increasing resolution. Here, we review how recent work using cutting-edge cryo-ET technologies is starting to provide fresh views into different aspects of cellular biology at an unprecedented level of detail. We anticipate that these developments will soon make cryo-ET a fundamental technique in cell biology.
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