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Pemberton JG, Tenkova T, Felgner P, Zimmerberg J, Balla T, Heuser J. Defining the EM-signature of successful cell-transfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583927. [PMID: 38496608 PMCID: PMC10942431 DOI: 10.1101/2024.03.07.583927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent structural changes after they have entered cells, changes that not only provide new insights into the mechanism of action of these particular transfection-reagents, but also provide a convenient and robust method for identifying by EM which cells in any culture have been successfully transfected. This also provides clues to the mechanism(s) of their toxic effects, when they are applied in excess. We demonstrate that after being bulk-endocytosed by cells, the cationic spheroids of Lipofectamine remain intact throughout the entire time of culturing, but escape from their endosomes and penetrate directly into the cytoplasm of the cell. In so doing, they provoke a stereotypical recruitment and rearrangement of endoplasmic reticulum (ER), and they ultimately end up escaping into the cytoplasm and forming unique 'inclusion-bodies.' Once free in the cytoplasm, they also invariably develop dense and uniform coatings of cytoplasmic ribosomes on their surfaces, and finally, they become surrounded by 'annulate' lamellae' of the ER. In the end, these annulate-lamellar enclosures become the ultrastructural 'signatures' of these inclusion-bodies, and serve to positively and definitively identify all cells that have been effectively transfected. Importantly, these new EM-observations define several new and unique properties of these classical Lipofectamines, and allow them to be discriminated from other lipoidal or particulate transfection-reagents, which we find do not physically break out of endosomes or end up in inclusion bodies, and in fact, provoke absolutely none of these 'signature' cytoplasmic reactions.
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Velle KB, Garner RM, Beckford TK, Weeda M, Liu C, Kennard AS, Edwards M, Fritz-Laylin LK. A conserved pressure-driven mechanism for regulating cytosolic osmolarity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.529730. [PMID: 36909496 PMCID: PMC10002747 DOI: 10.1101/2023.03.01.529730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Controlling intracellular osmolarity is essential to all cellular life. Cells that live in hypo-osmotic environments like freshwater must constantly battle water influx to avoid swelling until they burst. Many eukaryotic cells use contractile vacuoles to collect excess water from the cytosol and pump it out of the cell. Although contractile vacuoles are essential to many species, including important pathogens, the mechanisms that control their dynamics remain unclear. To identify basic principles governing contractile vacuole function, we here investigate the molecular mechanisms of two species with distinct vacuolar morphologies from different eukaryotic lineagesâ€"the discoban Naegleria gruberi , and the amoebozoan slime mold Dictyostelium discoideum . Using quantitative cell biology we find that, although these species respond differently to osmotic challenges, they both use actin for osmoregulation, as well as vacuolar-type proton pumps for filling contractile vacuoles. We also use analytical modeling to show that cytoplasmic pressure is sufficient to drive water out of contractile vacuoles in these species, similar to findings from the alveolate Paramecium multimicronucleatum . Because these three lineages diverged well over a billion years ago, we propose that this represents an ancient eukaryotic mechanism of osmoregulation.
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Affiliation(s)
- Katrina B. Velle
- Department of Biology, University of Massachusetts Amherst, Amherst, MA
| | - Rikki M. Garner
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | | | | | - Chunzi Liu
- Department of Applied Mathematics, Harvard University, Cambridge, MA
| | - Andrew S. Kennard
- Department of Biology, University of Massachusetts Amherst, Amherst, MA
| | - Marc Edwards
- Department of Biology, Amherst College, Amherst, MA
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Tahara YO, Miyata M. Visualization of Peptidoglycan Structures of Escherichia coli by Quick-Freeze Deep-Etch Electron Microscopy. Methods Mol Biol 2023; 2646:299-307. [PMID: 36842124 DOI: 10.1007/978-1-0716-3060-0_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall that protects the cell from turgor pressure and maintains its shape. In diderm (gram-negative) bacteria, such as Escherichia coli, the PG layer is flexible with a thickness of a 2-6 nm, and its visualization is difficult due to the presence of the outer membrane. The quick-freeze deep-etch replica method has been widely used for the visualization of flexible structures in cell interior, such as cell organelles and membrane components. In this technique, a platinum replica on the surface of a specimen fixed by freezing is observed using a transmission electron microscope. In this chapter, we describe the application of this method for visualizing the E. coli PG layer. We expect that these methods will be useful for the visualization of the PG layer in diverse bacterial species.
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Affiliation(s)
- Yuhei O Tahara
- Graduate School of Science, Osaka City University, Osaka, Japan. .,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan. .,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan.
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
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4
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Discovery of sex in an extremophilic red alga. Proc Natl Acad Sci U S A 2022; 119:e2216012119. [PMID: 36269868 PMCID: PMC9636976 DOI: 10.1073/pnas.2216012119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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5
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Sasajima Y, Kato T, Miyata T, Kawamoto A, Namba K, Miyata M. Isolation and structure of the fibril protein, a major component of the internal ribbon for Spiroplasma swimming. Front Microbiol 2022; 13:1004601. [PMID: 36274716 PMCID: PMC9582952 DOI: 10.3389/fmicb.2022.1004601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Spiroplasma, which are known pathogens and commensals of arthropods and plants, are helical-shaped bacteria that lack a peptidoglycan layer. Spiroplasma swim by alternating between left- and right-handed helicity. Of note, this system is not related to flagellar motility, which is widespread in bacteria. A helical ribbon running along the inner side of the helical cell should be responsible for cell helicity and comprises the bacterial actin homolog, MreB, and a protein specific to Spiroplasma, fibril. Here, we isolated the ribbon and its major component, fibril filament, for electron microscopy (EM) analysis. Single-particle analysis of the fibril filaments using the negative-staining EM revealed a three-dimensional chain structure composed of rings with a size of 11 nm wide and 6 nm long, connected by a backbone cylinder with an 8.7 nm interval with a twist along the filament axis. This structure was verified through EM tomography of quick-freeze deep-etch replica sample, with a focus on its handedness. The handedness and pitch of the helix for the isolated ribbon and fibril filament agreed with those of the cell in the resting state. Structures corresponding to the alternative state were not identified. These results suggest that the helical cell structure is supported by fibril filaments; however, the helical switch is caused by the force generated by the MreB proteins. The isolation and structural outline of the fibril filaments provide crucial information for an in-depth clarification of the unique swimming mechanism of Spiroplasma.
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Affiliation(s)
- Yuya Sasajima
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan,RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Osaka, Japan,*Correspondence: Makoto Miyata,
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Ohshima H, Mishima K, Amizuka N. Oral biosciences: The annual review 2021. J Oral Biosci 2022; 64:1-7. [PMID: 35143953 DOI: 10.1016/j.job.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND The Journal of Oral Biosciences is devoted to advancing and disseminating fundamental knowledge concerning every aspect of oral biosciences. HIGHLIGHT This review features review articles in the fields of "Extracellular Vesicles," "Propolis," "Odontogenic Tumors," "Periodontitis," "Periodontium," "Flavonoids," "Lactoferrin," "Dental Plaque," "Anatomy," "Induced Pluripotent Stem Cells," "Bone Cell Biology," "Dysgeusia," "Dental Caries," and "Dental Pulp Cavity," in addition to the review article by the winners of the "Lion Award" ("Sox9 function in salivary gland development") presented by the Japanese Association for Oral Biology. CONCLUSION These reviews in the Journal of Oral Biosciences have inspired its readers to broaden their knowledge regarding various aspects of oral biosciences. The current editorial review introduces these exciting review articles.
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Affiliation(s)
- Hayato Ohshima
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-ku, Niigata, 951-8514, Japan.
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Norio Amizuka
- Department of Developmental Biology of Hard Tissue, Graduate School of Dental Medicine, Faculty of Dental Medicine, Hokkaido University, Kita 13 Nishi 7 Kita-ku, Sapporo, 060-8586, Japan
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Leterrier C. A Pictorial History of the Neuronal Cytoskeleton. J Neurosci 2021; 41:11-27. [PMID: 33408133 PMCID: PMC7786211 DOI: 10.1523/jneurosci.2872-20.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
- Christophe Leterrier
- Aix Marseille Université, Centre National de la Recherche Scientifique, INP Unité Mixte de Recherche 7051, NeuroCyto, Marseille 13005, France
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Tahara YO, Miyata M, Nakamura T. Quick-Freeze, Deep-Etch Electron Microscopy Reveals the Characteristic Architecture of the Fission Yeast Spore. J Fungi (Basel) 2020; 7:jof7010007. [PMID: 33375328 PMCID: PMC7823873 DOI: 10.3390/jof7010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/28/2022] Open
Abstract
The spore of the fission yeast Schizosaccharomyces pombe is a dormant cell that is resistant to a variety of environmental stresses. The S. pombe spore is coated by a proteinaceous surface layer, termed the Isp3 layer because it comprises mainly Isp3 protein. Although thin-section electron microscopy and scanning electron microscopy have revealed the fundamental structure of the spore, its architecture remains unclear. Here we visualized S. pombe spores by using a quick-freeze replica electron microscopy (QFDE-EM) at nanometer resolution, which revealed novel characteristic structures. QFDE-EM revealed that the Isp3 layer exists as an interwoven fibrillar layer. On the spore cell membrane, many deep invaginations, which are longer than those on the vegetative cell membrane, are aligned in parallel. We also observed that during spore germination, the cell surface changes from a smooth to a dendritic filamentous structure, the latter being characteristic of vegetative cells. These findings provide significant insight into not only the structural composition of the spore, but also the mechanism underlying the stress response of the cell.
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Affiliation(s)
- Yuhei O. Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan;
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan;
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
- Correspondence: (M.M.); (T.N.)
| | - Taro Nakamura
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan;
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
- Correspondence: (M.M.); (T.N.)
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9
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Zhang B, Teraguchi E, Imada K, Tahara YO, Nakamura S, Miyata M, Kagiwada S, Nakamura T. The Fission Yeast RNA-Binding Protein Meu5 Is Involved in Outer Forespore Membrane Breakdown during Spore Formation. J Fungi (Basel) 2020; 6:jof6040284. [PMID: 33202882 PMCID: PMC7712723 DOI: 10.3390/jof6040284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
In Schizosaccharomyces pombe, the spore wall confers strong resistance against external stress. During meiosis II, the double-layered intracellular forespore membrane (FSM) forms de novo and encapsulates the nucleus. Eventually, the inner FSM layer becomes the plasma membrane of the spore, while the outer layer breaks down. However, the molecular mechanism and biological significance of this membrane breakdown remain unknown. Here, by genetic investigation of an S. pombe mutant (E22) with normal prespore formation but abnormal spores, we showed that Meu5, an RNA-binding protein known to bind to and stabilize more than 80 transcripts, is involved in this process. We confirmed that the E22 mutant does not produce Meu5 protein, while overexpression of meu5+ in E22 restores the sporulation defect. Furthermore, electron microscopy revealed that the outer membrane of the FSM persisted in meu5∆ spores. Investigation of the target genes of meu5+ showed that a mutant of cyc1+ encoding cytochrome c also showed a severe defect in outer FSM breakdown. Lastly, we determined that outer FSM breakdown occurs coincident with or after formation of the outermost Isp3 layer of the spore wall. Collectively, our data provide novel insights into the molecular mechanism of spore formation.
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Affiliation(s)
- Bowen Zhang
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
| | - Erika Teraguchi
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
| | - Kazuki Imada
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- Department of Chemistry and Biochemistry, National Institute of Technology, Suzuka College, Suzuka 510-0294, Japan
| | - Yuhei O. Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shuko Nakamura
- Department of Biological Sciences, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan; (S.N.); (S.K.)
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Satoshi Kagiwada
- Department of Biological Sciences, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan; (S.N.); (S.K.)
| | - Taro Nakamura
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
- Correspondence:
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Multilamellar and Multivesicular Outer Membrane Vesicles Produced by a Buttiauxella agrestis tolB Mutant. Appl Environ Microbiol 2020; 86:AEM.01131-20. [PMID: 32801184 DOI: 10.1128/aem.01131-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Outer membrane vesicles (OMVs) are naturally released from Gram-negative bacteria and play important roles in various biological functions. Released vesicles are not uniform in shape, size, or characteristics, and little is known about this diversity of OMVs. Here, we show that deletion of tolB, which encodes a part of the Tol-Pal system, leads to the production of multiple types of vesicles and increases overall vesicle production in the high-vesicle-forming Buttiauxella agrestis type strain JCM 1090. The ΔtolB mutant produced small OMVs and multilamellar/multivesicular OMVs (M-OMVs) as well as vesicles with a striking similarity to the wild type. M-OMVs, previously undescribed, contained triple-lamellar membrane vesicles and multiple vesicle-incorporating vesicles. Ultracentrifugation enabled the separation and purification of each type of OMV released from the ΔtolB mutant, and visualization by quick-freeze deep-etch and replica electron microscopy indicated that M-OMVs are composed of several lamellar membranes. Visualization of intracellular compartments of ΔtolB mutant cells showed that vesicles were accumulated in the broad periplasm, which is probably due to the low linkage between the outer and inner membranes attributed to the Tol-Pal defect. The outer membrane was invaginating inward by wrapping a vesicle, and the precursor of M-OMVs existed in the cell. Thus, we demonstrated a novel type of bacterial OMV and showed that unconventional processes enable the B. agrestis ΔtolB mutant to form unique vesicles.IMPORTANCE Membrane vesicle (MV) formation has been recognized as a common mechanism in prokaryotes, and MVs play critical roles in intercellular interaction. However, a broad range of MV types and their multiple production processes make it difficult to gain a comprehensive understanding of MVs. In this work, using vesicle separation and electron microscopic analyses, we demonstrated that diverse types of outer membrane vesicles (OMVs) were released from an engineered strain, Buttiauxella agrestis JCM 1090T ΔtolB mutant. We also discovered a previously undiscovered type of vesicle, multilamellar/multivesicular outer membrane vesicles (M-OMVs), which were released by this mutant using unconventional processes. These findings have facilitated considerable progress in understanding MV diversity and expanding the utility of MVs in biotechnological applications.
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Ravi RT, Leung MR, Zeev-Ben-Mordehai T. Looking back and looking forward: contributions of electron microscopy to the structural cell biology of gametes and fertilization. Open Biol 2020; 10:200186. [PMID: 32931719 PMCID: PMC7536082 DOI: 10.1098/rsob.200186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Mammalian gametes-the sperm and the egg-represent opposite extremes of cellular organization and scale. Studying the ultrastructure of gametes is crucial to understanding their interactions, and how to manipulate them in order to either encourage or prevent their union. Here, we survey the prominent electron microscopy (EM) techniques, with an emphasis on considerations for applying them to study mammalian gametes. We review how conventional EM has provided significant insight into gamete ultrastructure, but also how the harsh sample preparation methods required preclude understanding at a truly molecular level. We present recent advancements in cryo-electron tomography that provide an opportunity to image cells in a near-native state and at unprecedented levels of detail. New and emerging cellular EM techniques are poised to rekindle exploration of fundamental questions in mammalian reproduction, especially phenomena that involve complex membrane remodelling and protein reorganization. These methods will also allow novel lines of enquiry into problems of practical significance, such as investigating unexplained causes of human infertility and improving assisted reproductive technologies for biodiversity conservation.
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Affiliation(s)
- Ravi Teja Ravi
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Miguel Ricardo Leung
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
- Division of Structural Biology, Wellcome Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, UK
| | - Tzviya Zeev-Ben-Mordehai
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
- Division of Structural Biology, Wellcome Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, UK
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12
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Sanz-Luque E, Bhaya D, Grossman AR. Polyphosphate: A Multifunctional Metabolite in Cyanobacteria and Algae. FRONTIERS IN PLANT SCIENCE 2020; 11:938. [PMID: 32670331 PMCID: PMC7332688 DOI: 10.3389/fpls.2020.00938] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/09/2020] [Indexed: 05/19/2023]
Abstract
Polyphosphate (polyP), a polymer of orthophosphate (PO4 3-) of varying lengths, has been identified in all kingdoms of life. It can serve as a source of chemical bond energy (phosphoanhydride bond) that may have been used by biological systems prior to the evolution of ATP. Intracellular polyP is mainly stored as granules in specific vacuoles called acidocalcisomes, and its synthesis and accumulation appear to impact a myriad of cellular functions. It serves as a reservoir for inorganic PO4 3- and an energy source for fueling cellular metabolism, participates in maintaining adenylate and metal cation homeostasis, functions as a scaffold for sequestering cations, exhibits chaperone function, covalently binds to proteins to modify their activity, and enables normal acclimation of cells to stress conditions. PolyP also appears to have a role in symbiotic and parasitic associations, and in higher eukaryotes, low polyP levels seem to impact cancerous proliferation, apoptosis, procoagulant and proinflammatory responses and cause defects in TOR signaling. In this review, we discuss the metabolism, storage, and function of polyP in photosynthetic microbes, which mostly includes research on green algae and cyanobacteria. We focus on factors that impact polyP synthesis, specific enzymes required for its synthesis and degradation, sequestration of polyP in acidocalcisomes, its role in cellular energetics, acclimation processes, and metal homeostasis, and then transition to its potential applications for bioremediation and medical purposes.
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Affiliation(s)
- Emanuel Sanz-Luque
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, United States
- Department of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
| | - Devaki Bhaya
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, United States
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, United States
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13
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Wietrzynski W, Schaffer M, Tegunov D, Albert S, Kanazawa A, Plitzko JM, Baumeister W, Engel BD. Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision. eLife 2020; 9:53740. [PMID: 32297859 PMCID: PMC7164959 DOI: 10.7554/elife.53740] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Previously, we used in situ cryo-electron tomography to reveal the native architecture of thylakoid membranes (Engel et al., 2015). Here, we leverage technical advances to resolve the individual protein complexes within these membranes. Combined with a new method to visualize membrane surface topology, we map the molecular landscapes of thylakoid membranes inside green algae cells. Our tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains. This new approach to charting thylakoid topology lays the foundation for dissecting photosynthetic regulation at the level of single protein complexes within the cell.
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Affiliation(s)
- Wojciech Wietrzynski
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Dimitry Tegunov
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Atsuko Kanazawa
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, United States
| | - Jürgen M Plitzko
- 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
| | - Benjamin D Engel
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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14
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Price DC, Goodenough UW, Roth R, Lee JH, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D. Analysis of an improved Cyanophora paradoxa genome assembly. DNA Res 2020; 26:287-299. [PMID: 31098614 PMCID: PMC6704402 DOI: 10.1093/dnares/dsz009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/30/2019] [Indexed: 12/12/2022] Open
Abstract
Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage.
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Affiliation(s)
- Dana C Price
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | | | - Robyn Roth
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Marek Mutwil
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Camilla Ferrari
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Fabio Facchinelli
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany
| | - Steven G Ball
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
| | - Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
| | - Cheong Xin Chan
- Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Nicole E Wagner
- Department of Biochemistry and Microbiology, Rutgers, Rutgers University, New Brunswick, NJ, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, Rutgers University, New Brunswick, NJ, USA
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15
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Smith NL, Coukouma AE, Jakubek RS, Asher SA. Mechanisms by Which Organic Solvent Exchange Transforms Responsive Pure Protein Hydrogels into Responsive Organogels. Biomacromolecules 2019; 21:839-853. [DOI: 10.1021/acs.biomac.9b01522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Natasha Lynn Smith
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Andrew Eagle Coukouma
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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16
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Kozel BA, Mecham RP. Elastic fiber ultrastructure and assembly. Matrix Biol 2019; 84:31-40. [PMID: 31669522 DOI: 10.1016/j.matbio.2019.10.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/22/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Studies over the years have described a filamentous structure to mature elastin that suggests a complicated packing arrangement of tropoelastin subunits. The currently accepted mechanism for tropoelastin assembly requires microfibrils to serve as a physical extracellular scaffold for alignment of tropoelastin monomers during and before crosslinking. However, recent evidence suggests that the initial stages of tropoelastin assembly occur within the cell or at unique assembly sites on the plasma membrane where tropoelastin self assembles to form elastin aggregates. Outside the cell, elastin aggregates transfer to growing elastic fibers in the extracellular matrix where tensional forces on microfibrils generated through cell movement help shape the growing fiber. Overall, these observations challenge the widely held idea that interaction between monomeric tropoelastin and microfibrils is a requirement for elastin assembly, and point to self-assembly of tropoelastin as a driving force in elastin maturation.
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Affiliation(s)
- Beth A Kozel
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert P Mecham
- Department of Cell Biology and Physiology, Washington University School of Medicine, Campus Box 8228, 660 South Euclid Ave, St. Louis, MO, 63110, USA.
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17
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Application of spherical substrate to observe bacterial motility machineries by Quick-Freeze-Replica Electron Microscopy. Sci Rep 2019; 9:14765. [PMID: 31611568 PMCID: PMC6791848 DOI: 10.1038/s41598-019-51283-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/19/2019] [Indexed: 11/28/2022] Open
Abstract
3-D Structural information is essential to elucidate the molecular mechanisms of various biological machineries. Quick-Freeze Deep-Etch-Replica Electron Microscopy is a unique technique to give very high-contrast surface profiles of extra- and intra-cellular apparatuses that bear numerous cellular functions. Though the global architecture of those machineries is primarily required to understand their functional features, it is difficult or even impossible to depict side- or highly-oblique views of the same targets by usual goniometry, inasmuch as the objects (e.g. motile microorganisms) are placed on conventional flat substrates. We introduced silica-beads as an alternative substrate to solve such crucial issue. Elongated Flavobacterium and globular Mycoplasmas cells glided regularly along the bead’s surface, similarly to those on a flat substrate. Quick-freeze replicas of those cells attached to the beads showed various views; side-, oblique- and frontal-views, enabling us to study not only global but potentially more detailed morphology of complicated architecture. Adhesion of the targets to the convex surface could give surplus merits to visualizing intriguing molecular assemblies within the cells, which is relevant to a variety of motility machinery of microorganisms.
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18
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Krystofiak ES, Heymann JB, Kachar B. Carbon replicas reveal double stranded structure of tight junctions in phase-contrast electron microscopy. Commun Biol 2019; 2:98. [PMID: 30886907 PMCID: PMC6414538 DOI: 10.1038/s42003-019-0319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
Replica-based freeze-fracture and freeze-etching electron microscopy methods provide surface topography information, particularly suited to studying membrane protein complexes in their native context. The fidelity and resolution of metal replicas is limited by the inherent property of metal atoms to crystallize. To overcome the limitations of metal replicas, we combined amorphous carbon replicas with phase-contrast electron microscopy. Using this approach, tight junction intramembrane fibrils were shown to have a double stranded morphology.
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Affiliation(s)
- Evan S Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.,Cell Imaging Shared Resource, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.
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19
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Goodenough U, Roth R, Kariyawasam T, He A, Lee JH. Epiplasts: Membrane Skeletons and Epiplastin Proteins in Euglenids, Glaucophytes, Cryptophytes, Ciliates, Dinoflagellates, and Apicomplexans. mBio 2018; 9:e02020-18. [PMID: 30377285 PMCID: PMC6212826 DOI: 10.1128/mbio.02020-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/03/2023] Open
Abstract
Animals and amoebae assemble actin/spectrin-based plasma membrane skeletons, forming what is often called the cell cortex, whereas euglenids and alveolates (ciliates, dinoflagellates, and apicomplexans) have been shown to assemble a thin, viscoelastic, actin/spectrin-free membrane skeleton, here called the epiplast. Epiplasts include a class of proteins, here called the epiplastins, with a head/medial/tail domain organization, whose medial domains have been characterized in previous studies by their low-complexity amino acid composition. We have identified two additional features of the medial domains: a strong enrichment of acid/base amino acid dyads and a predicted β-strand/random coil secondary structure. These features have served to identify members in two additional unicellular eukaryotic radiations-the glaucophytes and cryptophytes-as well as additional members in the alveolates and euglenids. We have analyzed the amino acid composition and domain structure of 219 epiplastin sequences and have used quick-freeze deep-etch electron microscopy to visualize the epiplasts of glaucophytes and cryptophytes. We define epiplastins as proteins encoded in organisms that assemble epiplasts, but epiplastin-like proteins, of unknown function, are also encoded in Insecta, Basidiomycetes, and Caulobacter genomes. We discuss the diverse cellular traits that are supported by epiplasts and propose evolutionary scenarios that are consonant with their distribution in extant eukaryotes.IMPORTANCE Membrane skeletons associate with the inner surface of the plasma membrane to provide support for the fragile lipid bilayer and an elastic framework for the cell itself. Several radiations, including animals, organize such skeletons using actin/spectrin proteins, but four major radiations of eukaryotic unicellular organisms, including disease-causing parasites such as Plasmodium, have been known to construct an alternative and essential skeleton (the epiplast) using a class of proteins that we term epiplastins. We have identified epiplastins in two additional radiations and present images of their epiplasts using electron microscopy. We analyze the sequences and secondary structure of 219 epiplastins and present an in-depth overview and analysis of their known and posited roles in cellular organization and parasite infection. An understanding of epiplast assembly may suggest therapeutic approaches to combat infectious agents such as Plasmodium as well as approaches to the engineering of useful viscoelastic biofilms.
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Affiliation(s)
- Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Robyn Roth
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Thamali Kariyawasam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amelia He
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Freeze fracture: new avenues for the ultrastructural analysis of cells in vitro. Histochem Cell Biol 2017; 149:3-13. [PMID: 29134300 DOI: 10.1007/s00418-017-1617-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2017] [Indexed: 01/02/2023]
Abstract
The ultrastructural analysis of biological membranes by freeze fracture has a 60-year tradition. In this review, we summarize the benefits of the freeze-fracture technique and review special structures analyzed by freeze fracture and by combined freeze-fracture replica immunogold labeling (FRIL) of cell cultures. In principle, every cellular membrane whether of cell suspensions, mono- or bilayers of cell cultures can be analyzed in freeze fracture. The combination of freeze fracture and immunogold labeling of the replica allows the ultrastructural identification of protein assemblies in combination with the molecular identification of their constituent proteins using specific antibodies. The analysis of fractured and labeled intramembrane particles enables determination of the arrangement and organization of proteins within the membrane due to the high resolution of the transmission electron microscope. Because of cell-specific ultrastructural features such as square arrays, identification of cell types can be performed in parallel. This review is aimed at presenting the possibilities of freeze fracture and FRIL in the high-resolution ultrastructural analysis of membrane proteins and their assembly in naïve, transfected or otherwise treated cultured cells. At the interface of molecular approaches and morphology, the application of FRIL in genetically modified cells provides a novel and intriguing aspect for their analysis.
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21
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McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth R, Lichtle C, Goodenough U, Bowler CP, Dupont CL, Allen AE. Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom. THE PLANT CELL 2017; 29:2047-2070. [PMID: 28765511 PMCID: PMC5590495 DOI: 10.1105/tpc.16.00910] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/06/2017] [Accepted: 07/29/2017] [Indexed: 05/03/2023]
Abstract
The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO3-). To investigate the cellular and genetic basis of diatom NO3- assimilation, we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum In NR-KO cells, N-assimilation was abolished although NO3- transport remained intact. Unassimilated NO3- accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO3- chloride channel transporters plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO3- Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO3-, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO3- addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO3- replete and deplete conditions.
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Affiliation(s)
- James K McCarthy
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Sarah R Smith
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Maxine Tan
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Hong Zheng
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Karen Beeri
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Robyn Roth
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Christian Lichtle
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR8197 INSERM U1024, 75005 Paris, France
| | - Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Chris P Bowler
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR8197 INSERM U1024, 75005 Paris, France
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037
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22
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A Cryosectioning Technique for the Observation of Intracellular Structures and Immunocytochemistry of Tissues in Atomic Force Microscopy (AFM). Sci Rep 2017; 7:6462. [PMID: 28743939 PMCID: PMC5526917 DOI: 10.1038/s41598-017-06942-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023] Open
Abstract
The use of cryosectioning facilitates the morphological analysis and immunocytochemistry of cells in tissues in atomic force microscopy (AFM). The cantilever can access all parts of a tissue sample in cryosections after the embedding medium (sucrose) has been replaced with phosphate-buffered saline (PBS), and this approach has enabled the production of a type of high-resolution image. The images resembled those obtained from freeze-etching replica electron microscopy (EM) rather than from thin-section EM. The AFM images showed disks stacked and enveloped by the cell membrane in rod photoreceptor outer segments (ROS) at EM resolution. In addition, ciliary necklaces on the surface of connecting cilium, three-dimensional architecture of synaptic ribbons, and the surface of the post-synaptic membrane facing the active site were revealed, which were not apparent using thin-section EM. AFM could depict the molecular binding of anti-opsin antibodies conjugated to a secondary fluorescent antibody bound to the disk membrane. The specific localization of the anti-opsin binding sites was verified through correlation with immunofluorescence signals in AFM combined with confocal fluorescence microscope. To prove reproducibility in other tissues besides retina, cryosectioning-AFM was also applied to elucidate molecular organization of sarcomere in a rabbit psoas muscle.
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23
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Limardo AJ, Sudek S, Choi CJ, Poirier C, Rii YM, Blum M, Roth R, Goodenough U, Church MJ, Worden AZ. Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton. Environ Microbiol 2017; 19:3219-3234. [PMID: 28585420 DOI: 10.1111/1462-2920.13812] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 12/17/2022]
Abstract
Bathycoccus and Ostreococcus are broadly distributed marine picoprasinophyte algae. We enumerated small phytoplankton using flow cytometry and qPCR assays for phylogenetically distinct Bathycoccus clades BI and BII and Ostreococcus clades OI and OII. Among 259 photic-zone samples from transects and time-series, Ostreococcus maxima occurred in the North Pacific coastal upwelling for OI (36 713 ± 1485 copies ml-1 ) and the Kuroshio Front for OII (50 189 ± 561 copies ml-1 ) and the two overlapped only in frontal regions. The Bathycoccus overlapped more often with maxima along Line-P for BI (10 667 ± 1299 copies ml-1 ) and the tropical Atlantic for BII (4125 ± 339 copies ml-1 ). Only BII and OII were detected at warm oligotrophic sites, accounting for 34 ± 13% of 1589 ± 448 eukaryotic phytoplankton cells ml-1 (annual average) at Station ALOHA's deep chlorophyll maximum. Significant distributional and molecular differences lead us to propose that Bathycoccus clade BII represents a separate species which tolerates higher temperature oceanic conditions than Bathycoccus prasinos (BI). Morphological differences were not evident, but quick-freeze deep-etch electron microscopy provided insight into Bathycoccus scale formation. Our results highlight the importance of quantitative seasonal abundance data for inferring ecological distributions and demonstrate significant, differential picoprasinophyte contributions in mesotrophic and open-ocean waters.
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Affiliation(s)
- Alexander J Limardo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Chang Jae Choi
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Marguerite Blum
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Robyn Roth
- Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
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24
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Ismail EN, Ruberti JW, Malek G. Quick-freeze/deep-etch electron microscopy visualization of the mouse posterior pole. Exp Eye Res 2017. [PMID: 28629927 DOI: 10.1016/j.exer.2017.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The mouse is one of the most commonly used mammalian systems to study human diseases. In particular it has been an invaluable tool to model a multitude of ocular pathologies affecting the posterior pole. The aim of this study was to create a comprehensive map of the ultrastructure of the mouse posterior pole using the quick-freeze/deep-etch method (QFDE). QFDE can produce detailed three-dimensional images of tissue structure and macromolecular moieties, without many of the artifacts introduced by structure-altering post-processing methods necessary to perform conventional transmission electron microscopy (cTEM). A total of 18 eyes from aged C57BL6/J mice were enucleated and the posterior poles were processed, either intact or with the retinal pigment epithelium (RPE) cell layer removed, for imaging by either QFDE or cTEM. QFDE images were correlated with cTEM cross-sections and en face images through the outer retina. Nicely preserved outer retinal architecture was observed with both methods, however, QFDE provided excellent high magnification imaging, with greater detail, of the apical, central, and basal planes of the RPE. Furthermore, key landmarks within Bruch's membrane, choriocapillaris, choroid and sclera were characterized and identified. In this study we developed methods for preparing the outer retina of the mouse for evaluation with QFDE and provide a map of the ultrastructure and cellular composition of the outer posterior pole. This technique should be applicable for morphological evaluation of mouse models, in which detailed visualization of subtle ocular structural changes is needed or in cases where post-processing methods introduce unacceptable artifacts.
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Affiliation(s)
- Ebraheim N Ismail
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Jeffrey W Ruberti
- Department of Bioengineering, Northeastern University, Boston, MA, United States; Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, MA, United States.
| | - Goldis Malek
- Departments of Ophthalmology and Pathology, Duke University School of Medicine, Durham, NC, United States.
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25
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Trussart M, Yus E, Martinez S, Baù D, Tahara YO, Pengo T, Widjaja M, Kretschmer S, Swoger J, Djordjevic S, Turnbull L, Whitchurch C, Miyata M, Marti-Renom MA, Lluch-Senar M, Serrano L. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae. Nat Commun 2017; 8:14665. [PMID: 28272414 PMCID: PMC5344976 DOI: 10.1038/ncomms14665] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/20/2017] [Indexed: 12/24/2022] Open
Abstract
DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.
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Affiliation(s)
- Marie Trussart
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eva Yus
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Sira Martinez
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Davide Baù
- Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Yuhei O Tahara
- Department of Biology, Graduate School of Science, Osaka City University, 558-8585 Osaka, Japan.,OCU Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University, 558-8585 Osaka, Japan
| | - Thomas Pengo
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Michael Widjaja
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Simon Kretschmer
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Jim Swoger
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Steven Djordjevic
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Lynne Turnbull
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Cynthia Whitchurch
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, 558-8585 Osaka, Japan.,OCU Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University, 558-8585 Osaka, Japan
| | - Marc A Marti-Renom
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Luís Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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26
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The sleeping beauty kissed awake: new methods in electron microscopy to study cellular membranes. Biochem J 2017; 474:1041-1053. [DOI: 10.1042/bcj20160990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/03/2017] [Accepted: 01/23/2017] [Indexed: 01/12/2023]
Abstract
Electron microscopy (EM) for biological samples, developed in the 1940–1950s, changed our conception about the architecture of eukaryotic cells. It was followed by a period where EM applied to cell biology had seemingly fallen asleep, even though new methods with important implications for modern EM were developed. Among these was the discovery that samples can be preserved by chemical fixation and most importantly by rapid freezing without the formation of crystalline ice, giving birth to the world of cryo-EM. The past 15–20 years are hallmarked by a tremendous interest in EM, driven by important technological advances. Cryo-EM, in particular, is now capable of revealing structures of proteins at a near-atomic resolution owing to improved sample preparation methods, microscopes and cameras. In this review, we focus on the challenges associated with the imaging of membranes by EM and give examples from the field of host–pathogen interactions, in particular of virus-infected cells. Despite the advantages of imaging membranes under native conditions in cryo-EM, conventional EM will remain an important complementary method, in particular if large volumes need to be imaged.
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27
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Russo CJ, Scotcher S, Kyte M. A precision cryostat design for manual and semi-automated cryo-plunge instruments. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:114302. [PMID: 27910462 PMCID: PMC5270774 DOI: 10.1063/1.4967864] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Here we describe a bench-top cryostat system to control the temperature of liquid ethane in a cryo-plunge apparatus designed for biological specimen preparation for electron cryomicroscopy. It comprises a foam insulated Dewar containing a copper cryostat cup, whose temperature is controlled via an active feedback system to within 0.1 K. The device can easily be incorporated into existing manual and semi-automatic cryo-plunge instruments that are not equipped with cryogenic temperature control. Over the course of normal use, we find that using a cryostat is convenient, fast, and does not require special mixtures of cryogens like ethane/propane. This simple cryostat improves the reliability and reproducibility of biological specimen preparation for electron cryomicroscopy.
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Affiliation(s)
- Christopher J. Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Steve Scotcher
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin Kyte
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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28
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Makihara M, Watanabe T, Usukura E, Kaibuchi K, Narita A, Tanaka N, Usukura J. A new approach for the direct visualization of the membrane cytoskeleton in cryo-electron microscopy: a comparative study with freeze-etching electron microscopy. Microscopy (Oxf) 2016; 65:488-498. [PMID: 27587510 DOI: 10.1093/jmicro/dfw037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/10/2016] [Indexed: 12/17/2022] Open
Abstract
An improved unroofing method consisting of tearing off the cell membrane using an adhesive electron microscopy (EM) grid instead of vitreous ice sectioning (cryo-sectioning) has enabled us to panoramically view the membrane cytoskeleton in its native state with extremely high contrast. Grids pre-treated with Alcian blue were placed on cells, and a portion of the dorsal plasma membrane was transferred onto the grid, which was then floated in buffer solution. These membrane fragments contained sufficient cytoskeleton and were of suitable thickness for observation by cryo-EM. Many actin filaments and microtubules were clearly observed on the cytoplasmic surface of the plasma membrane with extremely high contrast because the soluble components of the cytoplasm flowed out and broke away from the cells. Actin filaments extended in all directions in a smooth contour with little branching. Microtubules spread out as far as 3 µm or more while winding gently in their native state. Upon fixation with 1% glutaraldehyde, however, the microtubules became straight and fragmented. Cryo-EM revealed for the first time a smooth endoplasmic reticulum network beneath the cell membrane in native cells. Clathrin coats and caveolae were also observed on the cytoplasmic surface of the plasma membrane, similar to those seen using freeze-etching replica EM (freeze-etching EM). Unroofing was also useful for immuno-labelling in cryo-EM. Antibody-labelled IQGAP1, one of the effector proteins facilitating the formation of actin filament networks, was localized alongside actin filaments. Freeze-etching EM confirmed the morphological findings of cryo-EM.
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Affiliation(s)
| | - Takashi Watanabe
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550
| | - Eiji Usukura
- Structural Biology Research Center, Nagoya University, Nagoya 464-8603
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550
| | - Akihiro Narita
- Structural Biology Research Center, Nagoya University, Nagoya 464-8603
| | - Nobuo Tanaka
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan
| | - Jiro Usukura
- Structural Biology Research Center, Nagoya University, Nagoya 464-8603
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29
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Zhang X, Wang Y. Glycosylation Quality Control by the Golgi Structure. J Mol Biol 2016; 428:3183-3193. [PMID: 26956395 PMCID: PMC4983240 DOI: 10.1016/j.jmb.2016.02.030] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/27/2016] [Accepted: 02/28/2016] [Indexed: 01/04/2023]
Abstract
Glycosylation is a ubiquitous modification that occurs on proteins and lipids in all living cells. Consistent with their high complexity, glycans play crucial biological roles in protein quality control and recognition events. Asparagine-linked protein N-glycosylation, the most complex glycosylation, initiates in the endoplasmic reticulum and matures in the Golgi apparatus. This process not only requires an accurate distribution of processing machineries, such as glycosyltransferases, glycosidases, and nucleotide sugar transporters, but also needs an efficient and well-organized factory that is responsible for the fidelity and quality control of sugar chain processing. In addition, accurate glycosylation must occur in coordination with protein trafficking and sorting. These activities are carried out by the Golgi apparatus, a membrane organelle in the center of the secretory pathway. To accomplish these tasks, the Golgi has developed into a unique stacked structure of closely aligned, flattened cisternae in which Golgi enzymes reside; in mammalian cells, dozens of Golgi stacks are often laterally linked into a ribbon-like structure. Here, we review our current knowledge of how the Golgi structure is formed and why its formation is required for accurate glycosylation, with the focus on how the Golgi stacking factors GRASP55 and GRASP65 generate the Golgi structure and how the conserved oligomeric Golgi complex maintains Golgi enzymes in different Golgi subcompartments by retrograde protein trafficking.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA; Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, USA.
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30
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Usukura E, Narita A, Yagi A, Ito S, Usukura J. An Unroofing Method to Observe the Cytoskeleton Directly at Molecular Resolution Using Atomic Force Microscopy. Sci Rep 2016; 6:27472. [PMID: 27273367 PMCID: PMC4895337 DOI: 10.1038/srep27472] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/19/2016] [Indexed: 11/09/2022] Open
Abstract
An improved unroofing method enabled the cantilever of an atomic force microscope (AFM) to reach directly into a cell to visualize the intracellular cytoskeletal actin filaments, microtubules, clathrin coats, and caveolae in phosphate-buffered saline (PBS) at a higher resolution than conventional electron microscopy. All of the actin filaments clearly exhibited a short periodicity of approximately 5-6 nm, which was derived from globular actins linked to each other to form filaments, as well as a long helical periodicity. The polarity of the actin filaments appeared to be determined by the shape of the periodic striations. Microtubules were identified based on their thickness. Clathrin coats and caveolae were observed on the cytoplasmic surface of cell membranes. The area containing clathrin molecules and their terminal domains was directly visualized. Characteristic ridge structures located at the surface of the caveolae were observed at high resolution, similar to those observed with electron microscopy (EM). Overall, unroofing allowed intracellular AFM imaging in a liquid environment with a level of quality equivalent or superior to that of EM. Thus, AFMs are anticipated to provide cutting-edge findings in cell biology and histology.
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Affiliation(s)
- Eiji Usukura
- Structural Biology Research Centre, Graduate School of Science, Nagoya University, Nagoya, 464-8603 Japan
| | - Akihiro Narita
- Structural Biology Research Centre, Graduate School of Science, Nagoya University, Nagoya, 464-8603 Japan
| | - Akira Yagi
- Olympus Corporation, Hachioji, Tokyo, 192-8512 Japan
| | - Shuichi Ito
- Olympus Corporation, Hachioji, Tokyo, 192-8512 Japan
| | - Jiro Usukura
- Structural Biology Research Centre, Graduate School of Science, Nagoya University, Nagoya, 464-8603 Japan
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31
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A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle. Proc Natl Acad Sci U S A 2016; 113:5958-63. [PMID: 27166422 DOI: 10.1073/pnas.1522866113] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological carbon fixation is a key step in the global carbon cycle that regulates the atmosphere's composition while producing the food we eat and the fuels we burn. Approximately one-third of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid. The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances carbon fixation by supplying Rubisco with a high concentration of CO2 Since the discovery of the pyrenoid more that 130 y ago, the molecular structure and biogenesis of this ecologically fundamental organelle have remained enigmatic. Here we use the model green alga Chlamydomonas reinhardtii to discover that a low-complexity repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco to form the pyrenoid. We find that EPYC1 is of comparable abundance to Rubisco and colocalizes with Rubisco throughout the pyrenoid. We show that EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2 We explain the central role of EPYC1 in pyrenoid biogenesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1's four repeats could produce the observed lattice arrangement of Rubisco in the Chlamydomonas pyrenoid. Our results suggest a surprisingly simple molecular mechanism for how Rubisco can be packaged to form the pyrenoid matrix, potentially explaining how Rubisco packaging into a pyrenoid could have evolved across a broad range of photosynthetic eukaryotes through convergent evolution. In addition, our findings represent a key step toward engineering a pyrenoid into crops to enhance their carbon fixation efficiency.
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32
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Zhang X, Wang Y. GRASPs in Golgi Structure and Function. Front Cell Dev Biol 2016; 3:84. [PMID: 26779480 PMCID: PMC4701983 DOI: 10.3389/fcell.2015.00084] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/14/2015] [Indexed: 12/26/2022] Open
Abstract
The Golgi apparatus is a central intracellular membrane organelle for trafficking and modification of proteins and lipids. Its basic structure is a stack of tightly aligned flat cisternae. In mammalian cells, dozens of stacks are concentrated in the pericentriolar region and laterally connected to form a ribbon. Despite extensive research in the last decades, how this unique structure is formed and why its formation is important for proper Golgi functioning remain largely unknown. The Golgi ReAssembly Stacking Proteins, GRASP65, and GRASP55, are so far the only proteins shown to function in Golgi stacking. They are peripheral membrane proteins on the cytoplasmic face of the Golgi cisternae that form trans-oligomers through their N-terminal GRASP domain, and thereby function as the “glue” to stick adjacent cisternae together into a stack and to link Golgi stacks into a ribbon. Depletion of GRASPs in cells disrupts the Golgi structure and results in accelerated protein trafficking and defective glycosylation. In this minireview we summarize our current knowledge on how GRASPs function in Golgi structure formation and discuss why Golgi structure formation is important for its function.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of MichiganAnn Arbor, MI, USA; Department of Neurology, University of Michigan School of MedicineAnn Arbor, MI, USA
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33
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Mohieldin AM, AbouAlaiwi WA, Gao M, Nauli SM. Chemical-Free Technique to Study the Ultrastructure of Primary Cilium. Sci Rep 2015; 5:15982. [PMID: 26521680 PMCID: PMC4629161 DOI: 10.1038/srep15982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/07/2015] [Indexed: 12/04/2022] Open
Abstract
A primary cilium is a hair-like structure with a width of approximately 200 nm. Over the past few decades, the main challenge in the study of the ultrastructure of cilia has been the high sensitivity of cilia to chemical fixation, which is required for many imaging techniques. In this report, we demonstrate a combined high-pressure freezing (HPF) and freeze-fracture transmission electron microscopy (FFTEM) technique to examine the ultrastructure of a cilium. Our objective is to develop an optimal high-resolution imaging approach that preserves cilia structures in their best natural form without alteration of cilia morphology by chemical fixation interference. Our results showed that a cilium has a swelling-like structure (termed bulb), which was previously considered a fixation artifact. The intramembrane particles observed via HPF/FFTEM indicated the presence of integral membrane proteins and soluble matrix proteins along the ciliary bulb, which is part of an integral structure within the ciliary membrane. We propose that HPF/FFTEM is an important and more suitable chemical-free method to study the ultrastructure of primary cilia.
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Affiliation(s)
- Ashraf M Mohieldin
- Department of Biomedical &Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618.,Department of Urology, University of California at Irvine Medical Campus, Orange, CA 92868.,Department of Medicinal &Biological Chemistry, University of Toledo School of Pharmacy, Toledo, OH 43614
| | - Wissam A AbouAlaiwi
- Department of Medicinal &Biological Chemistry, University of Toledo School of Pharmacy, Toledo, OH 43614
| | - Min Gao
- Liquid Crystal Institute, Kent State University, Kent, OH 44242
| | - Surya M Nauli
- Department of Biomedical &Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618.,Department of Urology, University of California at Irvine Medical Campus, Orange, CA 92868.,Department of Medicinal &Biological Chemistry, University of Toledo School of Pharmacy, Toledo, OH 43614
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34
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Heuser JE. Some personal and historical notes on the utility of "deep-etch" electron microscopy for making cell structure/function correlations. Mol Biol Cell 2015; 25:3273-6. [PMID: 25360049 PMCID: PMC4214773 DOI: 10.1091/mbc.e14-05-1016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This brief essay talks up the advantages of metal replicas for electron microscopy and explains why they are still the best way to image frozen cells in the electron microscope. Then it explains our approach to freezing, namely the Van Harreveld trick of "slamming" living cells onto a supercold block of metal sprayed with liquid helium at -269ºC, and further talks up this slamming over the alternative of high-pressure freezing, which is much trickier but enjoys greater favor at the moment. This leads me to bemoan the fact that there are not more young investigators today who want to get their hands on electron microscopes and use our approach to get the most "true to life" views of cells out of them with a minimum of hassle. Finally, it ends with a few perspectives on my own career and concludes that, personally, I'm permanently stuck with the view of the "founding fathers" that cell ultrastructure will ultimately display and explain all of cell function, or as Palade said in his Nobel lecture,electron micrographs are "irresistible and half transparent … their meaning buried under only a few years of work," and "reasonable working hypotheses are already suggested by the ultrastructural organization itself."
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Affiliation(s)
- John E Heuser
- WPI Institute, Kyoto University, Kyoto 606-8501, Japan; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110
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35
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Eisosome Ultrastructure and Evolution in Fungi, Microalgae, and Lichens. EUKARYOTIC CELL 2015; 14:1017-42. [PMID: 26253157 DOI: 10.1128/ec.00106-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/30/2015] [Indexed: 01/01/2023]
Abstract
Eisosomes are among the few remaining eukaryotic cellular differentations that lack a defined function(s). These trough-shaped invaginations of the plasma membrane have largely been studied in Saccharomyces cerevisiae, in which their associated proteins, including two BAR domain proteins, have been identified, and homologues have been found throughout the fungal radiation. Using quick-freeze deep-etch electron microscopy to generate high-resolution replicas of membrane fracture faces without the use of chemical fixation, we report that eisosomes are also present in a subset of red and green microalgae as well as in the cysts of the ciliate Euplotes. Eisosome assembly is closely correlated with both the presence and the nature of cell walls. Microalgal eisosomes vary extensively in topology and internal organization. Unlike fungi, their convex fracture faces can carry lineage-specific arrays of intramembranous particles, and their concave fracture faces usually display fine striations, also seen in fungi, that are pitched at lineage-specific angles and, in some cases, adopt a broad-banded patterning. The conserved genes that encode fungal eisosome-associated proteins are not found in sequenced algal genomes, but we identified genes encoding two algal lineage-specific families of predicted BAR domain proteins, called Green-BAR and Red-BAR, that are candidate eisosome organizers. We propose a model for eisosome formation wherein (i) positively charged recognition patches first establish contact with target membrane regions and (ii) a (partial) unwinding of the coiled-coil conformation of the BAR domains then allows interactions between the hydrophobic faces of their amphipathic helices and the lipid phase of the inner membrane leaflet, generating the striated patterns.
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36
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Takayama Y, Inui Y, Sekiguchi Y, Kobayashi A, Oroguchi T, Yamamoto M, Matsunaga S, Nakasako M. Coherent X-Ray Diffraction Imaging of Chloroplasts from Cyanidioschyzon merolae by Using X-Ray Free Electron Laser. PLANT & CELL PHYSIOLOGY 2015; 56:1272-1286. [PMID: 25745031 DOI: 10.1093/pcp/pcv032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 06/04/2023]
Abstract
Coherent X-ray diffraction imaging (CXDI) is a lens-less technique for visualizing the structures of non-crystalline particles with the dimensions of submicrometer to micrometer at a resolution of several tens of nanometers. We conducted cryogenic CXDI experiments at 66 K to visualize the internal structures of frozen-hydrated chloroplasts of Cyanidioschyzon merolae using X-ray free electron laser (XFEL) as a coherent X-ray source. Chloroplast dispersed specimen disks at a number density of 7/(10×10 µm(2)) were flash-cooled with liquid ethane without staining, sectioning or chemical labeling. Chloroplasts are destroyed at atomic level immediately after the diffraction by XFEL pulses. Thus, diffraction patterns with a good signal-to-noise ratio from single chloroplasts were selected from many diffraction patterns collected through scanning specimen disks to provide fresh specimens into the irradiation area. The electron density maps of single chloroplasts projected along the direction of the incident X-ray beam were reconstructed by using the iterative phase-retrieval method and multivariate analyses. The electron density map at a resolution of 70 nm appeared as a C-shape. In addition, the fluorescence image of proteins stained with Flamingo™ dye also appeared as a C-shape as did the autofluorescence from Chl. The similar images suggest that the thylakoid membranes with an abundance of proteins distribute along the outer membranes of chloroplasts. To confirm the present results statistically, a number of projection structures must be accumulated through high-throughput data collection in the near future. Based on the results, we discuss the feasibility of XFEL-CXDI experiments in the structural analyses of cellular organelles.
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Affiliation(s)
- Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo. 679-5148 Japan These authors contributed equally to this work
| | - Yayoi Inui
- Department of Applied Biological Science Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan These authors contributed equally to this work
| | - Yuki Sekiguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo. 679-5148 Japan These authors contributed equally to this work
| | - Amane Kobayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo. 679-5148 Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo. 679-5148 Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo. 679-5148 Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo. 679-5148 Japan
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37
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Bruckner JJ, Zhan H, O'Connor-Giles KM. Advances in imaging ultrastructure yield new insights into presynaptic biology. Front Cell Neurosci 2015; 9:196. [PMID: 26052269 PMCID: PMC4440913 DOI: 10.3389/fncel.2015.00196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/05/2015] [Indexed: 11/13/2022] Open
Abstract
Synapses are the fundamental functional units of neural circuits, and their dysregulation has been implicated in diverse neurological disorders. At presynaptic terminals, neurotransmitter-filled synaptic vesicles are released in response to calcium influx through voltage-gated calcium channels activated by the arrival of an action potential. Decades of electrophysiological, biochemical, and genetic studies have contributed to a growing understanding of presynaptic biology. Imaging studies are yielding new insights into how synapses are organized to carry out their critical functions. The development of techniques for rapid immobilization and preservation of neuronal tissues for electron microscopy (EM) has led to a new renaissance in ultrastructural imaging that is rapidly advancing our understanding of synapse structure and function.
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Affiliation(s)
- Joseph J Bruckner
- Cell and Molecular Biology Training Program, University of Wisconsin-Madison Madison, WI, USA
| | - Hong Zhan
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison Madison, WI, USA
| | - Kate M O'Connor-Giles
- Cell and Molecular Biology Training Program, University of Wisconsin-Madison Madison, WI, USA ; Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison Madison, WI, USA ; Laboratory of Genetics, University of Wisconsin-Madison Madison, WI, USA
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38
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Dupont CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Venter JC, Allen AE. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME JOURNAL 2014; 9:1076-92. [PMID: 25333462 PMCID: PMC4410273 DOI: 10.1038/ismej.2014.198] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/20/2014] [Accepted: 09/01/2014] [Indexed: 12/16/2022]
Abstract
Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.
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Affiliation(s)
- Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - John P McCrow
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Ruben Valas
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
| | - Nathan Walworth
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Robyn Roth
- Department of Biology, Washington University, St Louis, MO, USA
| | - Shane L Hogle
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jing Bai
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Zackary I Johnson
- 1] Marine Laboratory, Nicholas School of the Environment, Beaufort, NC, USA [2] Biology Department, Duke University, Durham, NC, USA
| | | | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Katherine A Barbeau
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - J Craig Venter
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Andrew E Allen
- 1] Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA [2] Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
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Ultrastructure and composition of the Nannochloropsis gaditana cell wall. EUKARYOTIC CELL 2014; 13:1450-64. [PMID: 25239976 DOI: 10.1128/ec.00183-14] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Marine algae of the genus Nannochloropsis are promising producers of biofuel precursors and nutraceuticals and are also harvested commercially for aquaculture feed. We have used quick-freeze, deep-etch electron microscopy, Fourier transform infrared spectroscopy, and carbohydrate analyses to characterize the architecture of the Nannochloropsis gaditana (strain CCMP 526) cell wall, whose recalcitrance presents a significant barrier to biocommodity extraction. The data indicate a bilayer structure consisting of a cellulosic inner wall (~75% of the mass balance) protected by an outer hydrophobic algaenan layer. Cellulase treatment of walls purified after cell lysis generates highly enriched algaenan preparations without using the harsh chemical treatments typically used in algaenan isolation and characterization. Nannochloropsis algaenan was determined to comprise long, straight-chain, saturated aliphatics with ether cross-links, which closely resembles the cutan of vascular plants. Chemical identification of >85% of the isolated cell wall mass is detailed, and genome analysis is used to identify candidate biosynthetic enzymes.
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Miyaguchi K. Direct imaging electron microscopy (EM) methods in modern structural biology: overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules. Biol Cell 2014; 106:323-45. [PMID: 25040059 DOI: 10.1111/boc.201300081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 07/01/2014] [Indexed: 11/28/2022]
Abstract
Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X-ray crystallography and single-particle cryo-electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative-staining, rotary-shadowing and freeze-etching EM, which are categorised here as 'direct imaging EM methods'. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome-translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three-dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo.
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Affiliation(s)
- Katsuyuki Miyaguchi
- Shinsapporokeiaikai Hospital, 5-5-35 Ooyachihigashi, Atsubetsuku, Sapporo, 004-0041, Japan
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41
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Abstract
Freeze fracture depends on the property of frozen tissues or cells, when cracked open, to split along the hydrophobic interior of membranes, thus revealing broad panoramas of membrane interior. These large panoramas reveal the three-dimensional contours of membranes making the methods well suited to studying changes in membrane architecture. Freshly split membrane faces are visualized by platinum or tungsten shadowing and carbon backing to form a replica that is then cleaned of tissue and imaged by TEM. Etching, i.e., removal of ice from the frozen fractured specimen by sublimation prior to shadowing, can also reveal the true surfaces of the membrane as well as the extracellular matrix and cytoskeletal networks that contact the membranes. Since the resolution of detail in the metal replicas formed is 1-2 nm, these methods can also be used to visualize macromolecules or macromolecular assemblies either in situ or displayed on a mica surface. These methods are available for either specimens that have been chemically fixed or specimens that have been rapidly frozen without chemical intervention.
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Ramundo S, Casero D, Mühlhaus T, Hemme D, Sommer F, Crèvecoeur M, Rahire M, Schroda M, Rusch J, Goodenough U, Pellegrini M, Perez-Perez ME, Crespo JL, Schaad O, Civic N, Rochaix JD. Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control. THE PLANT CELL 2014; 26:2201-2222. [PMID: 24879428 PMCID: PMC4079378 DOI: 10.1105/tpc.114.124842] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/16/2014] [Accepted: 05/09/2014] [Indexed: 05/14/2023]
Abstract
Plastid protein homeostasis is critical during chloroplast biogenesis and responses to changes in environmental conditions. Proteases and molecular chaperones involved in plastid protein quality control are encoded by the nucleus except for the catalytic subunit of ClpP, an evolutionarily conserved serine protease. Unlike its Escherichia coli ortholog, this chloroplast protease is essential for cell viability. To study its function, we used a recently developed system of repressible chloroplast gene expression in the alga Chlamydomonas reinhardtii. Using this repressible system, we have shown that a selective gradual depletion of ClpP leads to alteration of chloroplast morphology, causes formation of vesicles, and induces extensive cytoplasmic vacuolization that is reminiscent of autophagy. Analysis of the transcriptome and proteome during ClpP depletion revealed a set of proteins that are more abundant at the protein level, but not at the RNA level. These proteins may comprise some of the ClpP substrates. Moreover, the specific increase in accumulation, both at the RNA and protein level, of small heat shock proteins, chaperones, proteases, and proteins involved in thylakoid maintenance upon perturbation of plastid protein homeostasis suggests the existence of a chloroplast-to-nucleus signaling pathway involved in organelle quality control. We suggest that this represents a chloroplast unfolded protein response that is conceptually similar to that observed in the endoplasmic reticulum and in mitochondria.
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Affiliation(s)
- Silvia Ramundo
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - David Casero
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Timo Mühlhaus
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm Germany
| | - Dorothea Hemme
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm Germany
| | - Frederik Sommer
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm Germany
| | - Michèle Crèvecoeur
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Michèle Rahire
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Michael Schroda
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm Germany
| | - Jannette Rusch
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Maria Esther Perez-Perez
- Instituto de Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas, Universidad de Sevilla, 41092 Sevilla, Spain
| | - José Luis Crespo
- Instituto de Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas, Universidad de Sevilla, 41092 Sevilla, Spain
| | - Olivier Schaad
- Genomics Platform, University of Geneva, 1211 Geneva, Switzerland Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Natacha Civic
- Genomics Platform, University of Geneva, 1211 Geneva, Switzerland
| | - Jean David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
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Observation of Neuronal Death In Vitro by SEM and Optical Microscopy. E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY 2014. [DOI: 10.1380/ejssnt.2014.179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Delgado L, Carrión O, Martínez G, López-Iglesias C, Mercadé E. The stack: a new bacterial structure analyzed in the Antarctic bacterium Pseudomonas deceptionensis M1(T) by transmission electron microscopy and tomography. PLoS One 2013; 8:e73297. [PMID: 24039905 PMCID: PMC3767748 DOI: 10.1371/journal.pone.0073297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/18/2013] [Indexed: 01/06/2023] Open
Abstract
In recent years, improvements in transmission electron microscopy (TEM) techniques and the use of tomography have provided a more accurate view of the complexity of the ultrastructure of prokaryotic cells. Cryoimmobilization of specimens by rapid cooling followed by freeze substitution (FS) and sectioning, freeze fracture (FF) and observation of replica, or cryoelectron microscopy of vitreous sections (CEMOVIS) now allow visualization of biological samples close to their native state, enabling us to refine our knowledge of already known bacterial structures and to discover new ones. Application of these techniques to the new Antarctic cold-adapted bacterium Pseudomonasdeceptionensis M1T has demonstrated the existence of a previously undescribed cytoplasmic structure that does not correspond to known bacterial inclusion bodies or membranous formations. This structure, which we term a “stack”, was mainly visualized in slow growing cultures of P. deceptionensis M1T and can be described as a set of stacked membranous discs usually arranged perpendicularly to the cell membrane, but not continuous with it, and found in variable number in different locations within the cell. Regardless of their position, stacks were mostly observed very close to DNA fibers. Stacks are not exclusive to P. deceptionensis M1T and were also visualized in slow-growing cultures of other bacteria. This new structure deserves further study using cryoelectron tomography to refine its configuration and to establish whether its function could be related to chromosome dynamics.
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Affiliation(s)
- Lidia Delgado
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Ornella Carrión
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Gema Martínez
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
- * E-mail: ; (CLL)
| | - Elena Mercadé
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
- * E-mail: ; (CLL)
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Abstract
In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered.
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Affiliation(s)
- Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
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46
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Effects of therapeutic ultrasound on the nuclear envelope and nuclear pore complexes. J Appl Biomed 2013. [DOI: 10.2478/v10136-012-0042-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Heuser J. John Heuser: capture the moment. Interview by Caitlin Sedwick. J Cell Biol 2012; 199:868-9. [PMID: 23229894 PMCID: PMC3518215 DOI: 10.1083/jcb.1996pi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Heuser uses quick-freeze, deep-etch electron microscopy to explore cellular ultrastructure.
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Colony organization in the green alga Botryococcus braunii (Race B) is specified by a complex extracellular matrix. EUKARYOTIC CELL 2012; 11:1424-40. [PMID: 22941913 DOI: 10.1128/ec.00184-12] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Botryococcus braunii is a colonial green alga whose cells associate via a complex extracellular matrix (ECM) and produce prodigious amounts of liquid hydrocarbons that can be readily converted into conventional combustion engine fuels. We used quick-freeze deep-etch electron microscopy and biochemical/histochemical analysis to elucidate many new features of B. braunii cell/colony organization and composition. Intracellular lipid bodies associate with the chloroplast and endoplasmic reticulum (ER) but show no evidence of being secreted. The ER displays striking fenestrations and forms a continuous subcortical system in direct contact with the cell membrane. The ECM has three distinct components. (i) Each cell is surrounded by a fibrous β-1, 4- and/or β-1, 3-glucan-containing cell wall. (ii) The intracolonial ECM space is filled with a cross-linked hydrocarbon network permeated with liquid hydrocarbons. (iii) Colonies are enclosed in a retaining wall festooned with a fibrillar sheath dominated by arabinose-galactose polysaccharides, which sequesters ECM liquid hydrocarbons. Each cell apex associates with the retaining wall and contributes to its synthesis. Retaining-wall domains also form "drapes" between cells, with some folding in on themselves and penetrating the hydrocarbon interior of a mother colony, partitioning it into daughter colonies. We propose that retaining-wall components are synthesized in the apical Golgi apparatus, delivered to apical ER fenestrations, and assembled on the surfaces of apical cell walls, where a proteinaceous granular layer apparently participates in fibril morphogenesis. We further propose that hydrocarbons are produced by the nonapical ER, directly delivered to the contiguous cell membrane, and pass across the nonapical cell wall into the hydrocarbon-based ECM.
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Structural correlates of cytoplasmic and chloroplast lipid body synthesis in Chlamydomonas reinhardtii and stimulation of lipid body production with acetate boost. EUKARYOTIC CELL 2011; 10:1592-606. [PMID: 22037181 DOI: 10.1128/ec.05242-11] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Light microscopy and deep-etch electron microscopy were used to visualize triacylglyceride (TAG)-filled lipid bodies (LBs) of the green eukaryotic soil alga Chlamydomonas reinhardtii, a model organism for biodiesel production. Cells growing in nitrogen-replete media contain small cytoplasmic lipid bodies (α-cyto-LBs) and small chloroplast plastoglobules. When starved for N, β-cyto-LB formation is massively stimulated. β-Cyto-LBs are intimately associated with both the endoplasmic reticulum membrane and the outer membrane of the chloroplast envelope, suggesting a model for the active participation of both organelles in β-cyto-LB biosynthesis and packaging. When sta6 mutant cells, blocked in starch biosynthesis, are N starved, they produce β-cyto-LBs and also chloroplast LBs (cpst-LBs) that are at least 10 times larger than plastoglobules and eventually engorge the chloroplast stroma. Production of β-cyto-LBs and cpst-LBs under the conditions we used is dependent on exogenous 20 mM acetate. We propose that the greater TAG yields reported for N-starved sta6 cells can be attributed to the strain's ability to produce cpst-LBs, a capacity that is lost when the mutant is complemented by a STA6 transgene. Provision of a 20 mM acetate "boost" during N starvation generates sta6 cells that become so engorged with LBs-at the expense of cytoplasm and most organelles-that they float on water even when centrifuged. This property could be a desirable feature for algal harvesting during biodiesel production.
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