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Mironov AA, Beznoussenko GV. Algorithm for Modern Electron Microscopic Examination of the Golgi Complex. Methods Mol Biol 2022; 2557:161-209. [PMID: 36512216 DOI: 10.1007/978-1-0716-2639-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.
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Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Yamada H, Sato-Okamoto M, Chibana H. Ultrastructural Examination of Mouse Glomerular Capillary Loop by Sandwich Freezing and Freeze-Substitution. Microscopy (Oxf) 2022; 71:289-296. [PMID: 35778971 DOI: 10.1093/jmicro/dfac031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 11/12/2022] Open
Abstract
Sandwich freezing is a method of rapid freezing by sandwiching specimens between two metal disks, and has been used for observing exquisite close-to-native ultrastructure of living yeast and bacteria. Recently, this method has been found to be useful for preserving cell images of glutaraldehyde-fixed animal and human tissues. In the present study, this method was applied to observe fine structure of mouse glomerular capillary loops. Morphometry was then performed, and the results were compared with the data obtained by in vivo cryotechnique, which may provide the closest ultrastructure to the native state of living tissue. The results show that the ultrastructure of glomerular capillary loops obtained by sandwich freezing-freeze substitution after glutaraldehyde fixation was close to that of the ultrastructure obtained by in vivo cryotechnique, not only in quality of cell image but also in quantitative morphometry. They indicate that the ultrastructure obtained by sandwich freezing-freeze-substitution after glutaraldehyde fixation may more closely reflect the living state of cells and tissues than conventional chemical fixation and dehydration at room temperature and conventional rapid freezing freeze-substitution of excised tissues without glutaraldehyde fixation. Sandwich freezing-freeze substitution technique should be used routinely as a standard method for observing close-to-native ultrastructure of biological specimens.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | | | - Katsuyuki Uematsu
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24, Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Michiyo Sato-Okamoto
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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3
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Yamaguchi M, Takahashi-Nakaguchi A, Uematsu K, Naito K, Sato-Okamoto M, Ishiwata K, Naraoka S, Chibana H. Electron Microscopy of Mouse Tissues by Sandwich Freezing and Freeze-Substitution. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | - Kumiko Naito
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital
| | | | - Kazuki Ishiwata
- Department of Endocrinology, Hematology and Gerontology, Chiba University Hospital
| | - Sakino Naraoka
- Graduate School of Science and Engineering, Advanced Science and Engineering Biology, Chiba University
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Multispecies populations of methanotrophic Methyloprofundus and cultivation of a likely dominant species from the Iheya North deep-sea hydrothermal field. Appl Environ Microbiol 2021; 88:e0075821. [PMID: 34788070 PMCID: PMC8788690 DOI: 10.1128/aem.00758-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Methyloprofundus clade is represented by uncultivated methanotrophic bacterial endosymbionts of deep-sea bathymodiolin mussels, but only a single free-living species has been cultivated to date. This study reveals the existence of free-living Methyloprofundus variants in the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. A clade-targeted amplicon analysis of the particulate methane monooxygenase gene (pmoA) detected 647 amplicon sequence variants (ASVs) of the Methyloprofundus clade in microbial communities newly formed in in situ colonization systems. Such systems were deployed at colonies of bathymodiolin mussels and a galatheoid crab in diffuse-flow areas. These ASVs were classified into 161 species-like groups. The proportion of the species-like groups representing endosymbionts of mussels was unexpectedly low. A methanotrophic bacterium designated INp10, a likely dominant species in the Methyloprofundus population in this field, was enriched in a biofilm formed in a methane-fed cultivation system operated at 10°C. Genomic characterization with the gene transcription data set of INp10 from the biofilm suggested traits advantageous to niche competition in environments, such as mobility, chemotaxis, biofilm formation, offensive and defensive systems, and hypoxia tolerance. The notable metabolic traits that INp10 shares with some Methyloprofundus members are the use of lanthanide-dependent XoxF as the sole methanol dehydrogenase due to the absence of the canonical MxaFI, the glycolytic pathway using fructose-6-phosphate aldolase instead of fructose-1,6-bisphosphate aldolase, and the potential to perform partial denitrification from nitrate under oxygen-limited conditions. These findings help us better understand the ecological strategies of this possibly widespread marine-specific methanotrophic clade. IMPORTANCE The Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough is characterized by abundant methane derived from organic-rich sediments and diverse chemosynthetic animal species, including those harboring methanotrophic bacterial symbionts, such as bathymodiolin mussels Bathymodiolus japonicus and “Bathymodiolus” platifrons and a galatheoid crab, Shinkaia crosnieri. Symbiotic methanotrophs have attracted significant attention, and yet free-living methanotrophs in this environment have not been studied in detail. We focused on the free-living Methyloprofundus spp. that thrive in this hydrothermal field and identified an unexpectedly large number of species-like groups in this clade. Moreover, we enriched and characterized a methanotroph whose genome sequence indicated that it corresponds to a new species in the genus Methyloprofundus. This species might be a dominant member of the indigenous Methyloprofundus population. New information on free-living Methyloprofundus populations suggests that the hydrothermal field is a promising locale at which to investigate the adaptive capacity and associated genetic diversity of Methyloprofundus spp.
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5
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Yamaguchi M, Taguchi M, Uematsu K, Takahashi-Nakaguchi A, Sato-Okamoto M, Chibana H. Sandwich freezing device for rapid freezing of viruses, bacteria, yeast, cultured cells and animal and human tissues in electron microscopy. Microscopy (Oxf) 2021; 70:215-223. [PMID: 33206169 DOI: 10.1093/jmicro/dfaa049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/14/2022] Open
Abstract
We have been using sandwich freezing of living yeast and bacteria followed by freeze-substitution for observing close-to-native ultrastructure of cells. Recently, sandwich freezing of glutaraldehyde-fixed cultured cells and human tissues have been found to give excellent preservation of ultrastructure of cells and tissues. These studies, however, have been conducted using a handmade sandwich freezing device and have been limited in a few laboratories. To spread the use of this method to other laboratories, we fabricated and commercialized a new sandwich freezing device. The new device is inexpensive, portable and sterilizable. It can be used to rapid-freeze viruses, bacteria, yeast, cultured cells and animal and human tissues to a depth of 0.2 mm if tissues are prefixed with glutaraldehyde. The commercial availability of this device will expand application of rapid freezing to wide range of biological materials.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Masaki Taguchi
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | - Katsuyuki Uematsu
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka 237-0063, Japan
| | | | - Michiyo Sato-Okamoto
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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6
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Yamaguchi M, Yamada H, Chibana H. Deep-Sea Bacteria Harboring Bacterial Endosymbionts in a Cytoplasm?: 3D Electron Microscopy by Serial Ultrathin Sectioning of Freeze-Substituted Specimen. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Hiroyuki Yamada
- The Research Institute of Tuberculosis, JATA (Japan Anti-Tuberculosis Association)
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7
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Yamaguchi M, Wakabayashi S, Nakamura Y, Matsue H, Hirao T, Aoki S, Yamashina S, Yamada H, Mamizu N, Furukawa H, Chibana H. Good Ultrastructural Preservation of Human Tissues and Cultured Cells by Glutaraldehyde Fixation, Sandwich Freezing, and Freeze-Substitution. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | - Yuumi Nakamura
- Department of Dermatology, Chiba University Graduate School of Medicine
| | - Hiroyuki Matsue
- Department of Dermatology, Chiba University Graduate School of Medicine
| | - Takuya Hirao
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
- Department of Pharmaceutical Sciences, International University of Health and Welfare
| | - Shigeki Aoki
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University
| | | | - Hiroyuki Yamada
- The Research Institute of Tuberculosis, JATA (Japan Anti-Tuberculosis Association)
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8
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KLF4 is required for suppression of histamine synthesis by polyamines during bone marrow-derived mast cell differentiation. PLoS One 2020; 15:e0229744. [PMID: 32101568 PMCID: PMC7043748 DOI: 10.1371/journal.pone.0229744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/13/2020] [Indexed: 11/19/2022] Open
Abstract
Mast cells have secretory granules containing chemical mediators such as histamine and play important roles in the immune system. Polyamines are essential factors for cellular processes such as gene expression and translation. It has been reported that secretory granules contain both histamine and polyamines, which have similar chemical structures and are produced from the metabolism of cationic amino acids. We investigated the effect of polyamine depletion on mast cells using bone marrow-derived mast cells (BMMCs). Polyamine depletion was induced using α-difluoromethylornithine (DFMO), an irreversible inhibitor of ornithine decarboxylase. DFMO treatment resulted in a significant reduction of cell number and abnormal secretory granules in BMMCs. Moreover, the cells showed a 2.3-fold increase in intracellular histamine and up-regulation of histidine decarboxylase (HDC) at the transcriptional level during BMMC differentiation. Levels of the transcription factor kruppel-like factor 4 (KLF4) greatly decreased upon DFMO treatment; however, Klf4 mRNA was expressed at levels similar to controls. We determined the translational regulation of KLF4 using reporter genes encoding Klf4-luc2 fusion mRNA, for transfecting NIH3T3 cells, and performed in vitro translation. We found that the efficiency of KLF4 synthesis in response to DFMO treatment was enhanced by the existence of a GC-rich 5'-untranslated region (5'-UTR) on Klf4 mRNA, regardless of the recognition of the initiation codon. Taken together, these results indicate that the enhancement of histamine synthesis by DFMO depends on the up-regulation of Hdc expression, achieved by removal of transcriptional suppression of KLF4, during differentiation.
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9
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Glycolytic suppression dramatically changes the intracellular metabolic profile of multiple cancer cell lines in a mitochondrial metabolism-dependent manner. Sci Rep 2019; 9:18699. [PMID: 31822748 PMCID: PMC6904735 DOI: 10.1038/s41598-019-55296-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
Most cancer cells rely on glycolysis to generate ATP, even when oxygen is available. However, merely inhibiting the glycolysis is insufficient for the eradication of cancer cells. One main reason for this is that cancer cells have the potential to adapt their metabolism to their environmental conditions. In this study, we investigated how cancer cells modify their intracellular metabolism when glycolysis is suppressed, using PANC-1 pancreatic cancer cells and two other solid tumor cell lines, A549 and HeLa. Our study revealed that glycolytically suppressed cells upregulated mitochondrial function and relied on oxidative phosphorylation (OXPHOS) to obtain the ATP necessary for their survival. Dynamic changes in intracellular metabolic profiles were also observed, reflected by the reduced levels of TCA cycle intermediates and elevated levels of most amino acids. Glutamine and glutamate were important for this metabolic reprogramming, as these were largely consumed by influx into the TCA cycle when the glycolytic pathway was suppressed. During the reprogramming process, activated autophagy was involved in modulating mitochondrial function. We conclude that upon glycolytic suppression in multiple types of tumor cells, intracellular energy metabolism is reprogrammed toward mitochondrial OXPHOS in an autophagy-dependent manner to ensure cellular survival.
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10
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Bushell SR, Pike ACW, Falzone ME, Rorsman NJG, Ta CM, Corey RA, Newport TD, Christianson JC, Scofano LF, Shintre CA, Tessitore A, Chu A, Wang Q, Shrestha L, Mukhopadhyay SMM, Love JD, Burgess-Brown NA, Sitsapesan R, Stansfeld PJ, Huiskonen JT, Tammaro P, Accardi A, Carpenter EP. The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K. Nat Commun 2019; 10:3956. [PMID: 31477691 PMCID: PMC6718402 DOI: 10.1038/s41467-019-11753-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum (ER) the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase or chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident lipid scramblase with a requirement for short chain lipids and calcium for robust activity. Crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional cryo-EM structures reveal extensive conformational changes from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity. TMEM16K is a member of the TMEM16 family of integral membrane proteins that are either lipid scramblases or chloride channels. Here the authors combine cell biology, electrophysiology measurements, X-ray crystallography, cryo-EM and MD simulations to structurally characterize TMEM16K and show that it is an ER-resident lipid scramblase.
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Affiliation(s)
- Simon R Bushell
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Nils J G Rorsman
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,OxSyBio, Atlas Building, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Chau M Ta
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,Department of Cardiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK.,Oxford Nanopore Technologies, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - John C Christianson
- Nuffield Department of Rheumatology, Orthopaedics and Musculoskeletal Sciences, University of Oxford, Windmill Road, Oxford, OX3 7LD, UK
| | - Lara F Scofano
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Chitra A Shintre
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Vertex Pharmaceuticals Ltd, Milton Park, Oxfordshire, OX14 4RW, UK
| | - Annamaria Tessitore
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Nuffield Division of Clinical Laboratory Sciences, Oxford University, Oxford, OX3 9DU, UK
| | - Amy Chu
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, Oxford University, Oxford, OX1 3QT, UK
| | - Qinrui Wang
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Leela Shrestha
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Shubhashish M M Mukhopadhyay
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - James D Love
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461-1602, USA.,Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Nicola A Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rebecca Sitsapesan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Paolo Tammaro
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Alessio Accardi
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA.,Department of Anesthesiology, Weill Cornell Medical School, 25 East 68th Street, New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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11
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Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. ISME JOURNAL 2019; 13:2465-2474. [PMID: 31171857 DOI: 10.1038/s41396-019-0447-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 01/07/2023]
Abstract
A deep-branching clade of Thaumarchaeota, conventionally called Terrestrial hot spring creanarchaeotic group (THSCG), is a missing link between thaumarchaeotic ammonia oxidizers and the deeper-branching non-ammonia oxidizers, such as Crenarchaeota and Candidatus Korarchaeota. Here, we report isolation of the first cultivated representative from the THSCG, named as NAS-02. Physiological characterization demonstrated that the isolate was a thermoacidophilic, sulfur- and iron-reducing organoheterotroph, which was supported by gene contents encoded in its complete genome. There was no evidence for ammonia oxidation by the isolate. Members in THSCG are likely thermophiles, and may play roles in degrading cell debris as a scavenger and in biogeochemical cycling of sulfur and iron in the hot environments, as suggested by the physiological characteristics of the isolate and the geographical distribution of the 16S rRNA gene sequences of THSCG in terrestrial hot springs and marine hydrothermal fields. Phylogenetic analysis suggests that the THSCG lineage represented by NAS-02 has gained the ability of sulfur reduction via horizontal gene transfer. Based on the phylogeny and physiology, we propose the name Conexivisphaera calidus gen. nov., sp. nov. to accommodate the isolate.
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12
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Wofford JD, Lindahl PA. A mathematical model of iron import and trafficking in wild-type and Mrs3/4ΔΔ yeast cells. BMC SYSTEMS BIOLOGY 2019; 13:23. [PMID: 30791941 PMCID: PMC6385441 DOI: 10.1186/s12918-019-0702-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 02/06/2019] [Indexed: 12/03/2022]
Abstract
Background Iron plays crucial roles in the metabolism of eukaryotic cells. Much iron is trafficked into mitochondria where it is used for iron-sulfur cluster assembly and heme biosynthesis. A yeast strain in which Mrs3/4, the high-affinity iron importers on the mitochondrial inner membrane, are deleted exhibits a slow-growth phenotype when grown under iron-deficient conditions. However, these cells grow at WT rates under iron-sufficient conditions. The object of this study was to develop a mathematical model that could explain this recovery on the molecular level. Results A multi-tiered strategy was used to solve an ordinary-differential-equations-based mathematical model of iron import, trafficking, and regulation in growing Saccharomyces cerevisiae cells. At the simplest level of modeling, all iron in the cell was presumed to be a single species and the cell was considered to be a single homogeneous volume. Optimized parameters associated with the rate of iron import and the rate of dilution due to cell growth were determined. At the next level of complexity, the cell was divided into three regions, including cytosol, mitochondria, and vacuoles, each of which was presumed to contain a single form of iron. Optimized parameters associated with import into these regions were determined. At the final level of complexity, nine components were assumed within the same three cellular regions. Parameters obtained at simpler levels of complexity were used to help solve the more complex versions of the model; this was advantageous because the data used for solving the simpler model variants were more reliable and complete relative to those required for the more complex variants. The optimized full-complexity model simulated the observed phenotype of WT and Mrs3/4ΔΔ cells with acceptable fidelity, and the model exhibited some predictive power. Conclusions The developed model highlights the importance of an FeII mitochondrial pool and the necessary exclusion of O2 in the mitochondrial matrix for eukaryotic iron-sulfur cluster metabolism. Similar multi-tiered strategies could be used for any micronutrient in which concentrations and metabolic forms have been determined in different organelles within a growing eukaryotic cell. Electronic supplementary material The online version of this article (10.1186/s12918-019-0702-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua D Wofford
- Texas A&M University, Department of Chemistry, College Station, TX, 77843-3255, USA
| | - Paul A Lindahl
- Texas A&M University, Department of Chemistry, College Station, TX, 77843-3255, USA. .,Texas A&M University, Department of Biochemistry & Biophysics, College Station, 77843-3255, USA.
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13
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Yamaguchi M, Yamada H, Uematsu K, Horinouchi Y, Chibana H. Electron Microscopy and Structome Analysis of Unique Amorphous Bacteria from the Deep Sea in Japan. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association
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14
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Hirao T, Yamaguchi M, Kikuya M, Chibana H, Ito K, Aoki S. Altered intracellular signaling by imatinib increases the anti-cancer effects of tyrosine kinase inhibitors in chronic myelogenous leukemia cells. Cancer Sci 2017; 109:121-131. [PMID: 29121435 PMCID: PMC5765287 DOI: 10.1111/cas.13442] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 10/28/2017] [Accepted: 11/02/2017] [Indexed: 12/15/2022] Open
Abstract
Tyrosine kinase inhibitors (TKI), including imatinib (IM), improve the outcome of CML therapy. However, TKI treatment is long‐term and can induce resistance to TKI, which often leads to a poor clinical outcome in CML patients. Here, we examined the effect of continuous IM exposure on intracellular energy metabolism in K562 cells, a human Philadelphia chromosome‐positive CML cell line, and its subsequent sensitivity to anti‐cancer agents. Contrary to our expectations, we found that continuous IM exposure increased sensitivity to TKI. Cancer energy metabolism, characterized by abnormal glycolysis, is linked to cancer cell survival. Interestingly, glycolytic activity was suppressed by continuous exposure to IM, and autophagy increased to maintain cell viability by compensating for glycolytic suppression. Notably, increased sensitivity to TKI was not caused by glycolytic inhibition but by altered intracellular signaling, causing glycolytic suppression and increased autophagy, as evidenced by suppression of p70 S6 kinase 1 (S6K1) and activation of AMP‐activated protein kinase (AMPK). Using another human CML cell line (KCL22 cells) and BCR/ABL+ Ba/F3 cells (mimicking Philadelphia chromosome‐positive CML cells) confirmed that suppressing S6K1 and activating AMPK increased sensitivity to TKI. Furthermore, suppressing S6K1 and activating AMPK had a synergistic anti‐cancer effect by inhibiting autophagy in the presence of TKI. The present study provides new insight into the importance of signaling pathways that affect cellular energy metabolism, and suggests that co‐treatment with agents that disrupt energy metabolic signaling (using S6K1 suppressors and AMPK activators) plus blockade of autophagy may be strategies for TKI‐based CML therapy.
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Affiliation(s)
- Takuya Hirao
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Megumi Kikuya
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Kousei Ito
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Shigeki Aoki
- Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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15
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Shift in energy metabolism caused by glucocorticoids enhances the effect of cytotoxic anti-cancer drugs against acute lymphoblastic leukemia cells. Oncotarget 2017; 8:94271-94285. [PMID: 29212227 PMCID: PMC5706873 DOI: 10.18632/oncotarget.21689] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy. Treatments include glucocorticoids (GCs) such as dexamethasone (Dex) and prednisolone, which may be of value when used alongside cytotoxic anti-cancer drugs. To predict therapeutic efficacy of GCs, their activity against ALL cells is usually examined prior to chemotherapy; however, few studies have examined their effects when used in combination with other drugs. The paradox is that cytotoxic anti-cancer drugs that are effective against proliferating cancer cells show synergistic effects when used with GCs that prevent cell proliferation. To address this point, we investigated intracellular energy metabolism in ALL CCRF-CEM cell clones classified according to their sensitivity to Dex and cytotoxic anti-cancer drugs in bulk cultures of mixed cells. We found that Dex suppressed glycolysis, the most important metabolic system in cancer cells, in cells that were damaged by etoposide (a cytotoxic anti-cancer drug), and the cells showed a concomitant increase in mitochondrial oxidative phosphorylation. Furthermore, autophagy, an intracellular bulk degradation system, regulated mitochondrial viability. We also found that mitochondria, whose function is enhanced by Dex, were susceptible to anti-cancer drugs that inhibit respiratory complexes (e.g., etoposide and daunorubicin), resulting in increased production of reactive oxygen species and subsequent cytotoxicity. Taken together, the present study points the way toward a more accurate prediction of the sensitivity of ALL cells to the combined action of anti-cancer drugs and GCs, by taking into consideration the shift in intracellular energy metabolism caused by GCs: namely, from glycolysis to mitochondrial oxidative phosphorylation mediated by autophagy.
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16
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Yamaguchi M, Takahashi-Nakaguchi A, Aida Y, Sato-Okamoto M, Chibana H. Convenient method for better preservation of fine structures of cultured macrophages and engulfed yeast cells by freeze-substitution fixation. Microscopy (Oxf) 2017; 66:209-211. [PMID: 28339650 DOI: 10.1093/jmicro/dfx006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023] Open
Abstract
Rapid freeze-freeze substitution after glutaraldehyde fixation (CF-FS method) obtained the natural and fine structures of macrophages and engulfed yeast cells. Culturing macrophages on single hole molybdenum grids placed in culture dishes made possible the rapid freezing of cells by the 'open sandwich method'. This method may be convenient when rapid-freezing cannot be performed immediately, or when a rapid-freezing device is not available in the lab.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku Chiba 260-8673,Japan
| | | | - Yuko Aida
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku Chiba 260-8673,Japan
| | - Michiyo Sato-Okamoto
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku Chiba 260-8673,Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku Chiba 260-8673,Japan
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17
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Toh-E A, Ohkusu M, Shimizu K, Yamaguchi M, Ishiwada N, Watanabe A, Kamei K. Creation, characterization and utilization of Cryptococcus neoformans mutants sensitive to micafungin. Curr Genet 2017; 63:1093-1104. [PMID: 28560585 DOI: 10.1007/s00294-017-0713-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 11/27/2022]
Abstract
We constructed deletion mutants of Cryptococcus neoformans var neoformans (serotype D) genes encoding late ergosterol biosynthetic pathway enzymes and found that the mutations enhanced susceptibility to various drugs including micafungin, one of the echinocandins, to which wild-type Cryptococcus strains show no susceptibility. Furthermore, through isolation of a mutant resistant to micafungin from a micafungin-sensitive erg mutant and genetic analysis of it, we found that the responsible mutation occurred in the hotspot 2 of FKS1 encoding β-1, 3-glucan synthase, indicating that micafungin inhibited the growth of the erg mutant via inhibiting Fks1 activity. Addition of ergosterol to the culture of the erg mutants recovered the resistance to micafungin, suggesting that the presence of ergosterol in membrane inhibits the accession of micafungin to its target. We found that a loss of one of genes encoding subunits of v-ATPase, VPH1, made Cryptococcus cells sensitive to micafungin. Our observation that the erg2 vph1 double mutant was more sensitive to micafungin than either single mutant suggests that these two genes act differently in becoming resistant to micafungin. The erg mutants allowed us to study the physiological significance of β-1, 3-glucan synthesis in C. neoformans; the inhibition of β-1, 3-glucan synthesis induced cell death and changes in cellular morphology. By observing the erg mutant cells recovering from the growth inhibition imposed by micafungin, we recognized β-1, 3-glucan synthesis would suppress filamentous growth in C. neoformans.
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Affiliation(s)
- Akio Toh-E
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chiba, 260-8673, Japan.
| | - Misako Ohkusu
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chiba, 260-8673, Japan
| | - Kiminori Shimizu
- Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chiba, 260-8673, Japan
| | - Naruhiko Ishiwada
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chiba, 260-8673, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chiba, 260-8673, Japan
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chiba, 260-8673, Japan
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18
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Yamaguchi M, Aoyama T, Yamada N, Chibana H. Quantitative measurement of hydrophilicity/hydrophobicity of the plasma-polymerized naphthalene film (Super Support Film) and other support films and grids in electron microscopy. Microscopy (Oxf) 2016; 65:444-450. [PMID: 27512014 DOI: 10.1093/jmicro/dfw031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/05/2016] [Indexed: 11/12/2022] Open
Abstract
Hydrophilicity/hydrophobicity of the surfaces of plasma-polymerized naphthalene film (Super Support Film, Nisshin EM Co. Ltd., Tokyo), carbon and formvar support films, and copper and nickel grids were quantitatively estimated by contact angles measured from diameters and heights of water droplets placed on various specimens. With treatment of glow discharge, the surfaces of plasma-polymerized naphthalene and carbon support films became fully hydrophilic in 20 s. They remained hydrophilic for 6 h. The surfaces of copper and nickel grids became fully hydrophilic with 60 s of glow discharge treatment. They remained hydrophilic for only 1 h. This information is useful for negative staining, ultrathin sectioning and rapid freezing of biological specimens using the sandwich method.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Toshihiro Aoyama
- National Institute of Technology, Suzuka College, Shirako-cho, Suzuka-shi, Mie 510-0294, Japan
| | - Norihiro Yamada
- Faculty of Educations, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba 263-8522, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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19
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Yamaguchi M, Yamada H, Higuchi K, Yamamoto Y, Arai S, Murata K, Mori Y, Furukawa H, Uddin MS, Chibana H. High-voltage electron microscopy tomography and structome analysis of unique spiral bacteria from the deep sea. Microscopy (Oxf) 2016; 65:363-9. [PMID: 27230559 DOI: 10.1093/jmicro/dfw016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 03/30/2016] [Indexed: 11/15/2022] Open
Abstract
Structome analysis is a useful tool for identification of unknown microorganisms that cannot be cultured. In 2012, we discovered a unique deep-sea microorganism with a cell structure intermediate between those of prokaryotes and eukaryotes and described its features using freeze-substitution electron microscopy and structome analysis (quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level). We named it Myojin parakaryote Here we describe, using serial ultrathin sectioning and high-voltage electron microscopy tomography of freeze-substituted specimens, the structome analysis and 3D reconstruction of another unique spiral bacteria, found in the deep sea off the coast of Japan. The bacteria, which is named as 'Myojin spiral bacteria' after the discovery location and their morphology, had a total length of 1.768 ± 0.478 µm and a total diameter of 0.445 ± 0.050 µm, and showed either clockwise or counter-clockwise spiral. The cells had a cell surface membrane, thick fibrous layer, ribosomes and inner fibrous structures (most likely DNA). They had no flagella. The bacteria had 322 ± 119 ribosomes per cell. This ribosome number is only 1.2% of that of Escherichia coli and 19.3% of Mycobacterium tuberculosis and may reflect a very slow growth rate of this organism in the deep sea.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo 204-8533, Japan
| | - Kimitaka Higuchi
- High Voltage Electron Microscopy Laboratory, Ecotopia Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Yuta Yamamoto
- High Voltage Electron Microscopy Laboratory, Ecotopia Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Shigeo Arai
- High Voltage Electron Microscopy Laboratory, Ecotopia Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Kazuyoshi Murata
- Section of Electron Microscopy, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Yuko Mori
- System in Frontier Inc., 2-8-3 Shinsuzuharu Bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan
| | - Hiromitsu Furukawa
- System in Frontier Inc., 2-8-3 Shinsuzuharu Bldg. 4F, Akebono-cho, Tachikawa-shi, Tokyo 190-0012, Japan
| | - Mohammad Shorif Uddin
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan Department of Computer Science and Engineering, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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20
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Kopecká M, Yamaguchi M, Kawamoto S. Effects of the F-actin inhibitor latrunculin A on the budding yeast Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2015; 161:1348-55. [PMID: 25858300 DOI: 10.1099/mic.0.000091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our basic cell biology research was aimed at investigating the effect on eukaryotic cells of the sudden loss of the F-actin cytoskeleton. Cells treated with latrunculin A (LA) in yeast extract peptone dextrose (YEPD) medium were examined using phase-contrast and fluorescent microscopy, freeze-substitution, transmission and scanning electron microscopy, counted using a Bürker chamber and their absorbance measured. The cells responded to the presence of LA, an F-actin inhibitor, with the disappearance of actin patches, actin cables and actin rings. This resulted in the formation of larger spherical cells with irregular morphology in the cell walls and ultrastructural disorder of the cell organelles and secretory vesicles. Instead of buds, LA-inhibited cells formed only 'table-mountain-like' wide flattened swellings without apical growth with a thinner glucan cell-wall layer containing β-1,3-glucan microfibrils. The LA-inhibited cells lysed. Actin cables and patches were required for bud formation and bud growth. In addition, actin patches were required for the formation of β-1,3-glucan microfibrils in the bud cell wall. LA has fungistatic, fungicidal and fungilytic effects on the budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Marie Kopecká
- 1Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Masashi Yamaguchi
- 2Medical Mycology Research Centre, Chiba University, Chuo-ku, Japan
| | - Susumu Kawamoto
- 2Medical Mycology Research Centre, Chiba University, Chuo-ku, Japan
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21
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Yamada H, Chikamatsu K, Aono A, Mitarai S. Pre-fixation of virulent Mycobacterium tuberculosis with glutaraldehyde preserves exquisite ultrastructure on transmission electron microscopy through cryofixation and freeze-substitution with osmium-acetone at ultralow temperature. J Microbiol Methods 2013; 96:50-5. [PMID: 24200708 DOI: 10.1016/j.mimet.2013.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 10/26/2022]
Abstract
Sample preparations for transmission electron microscopy of virulent Mycobacterium tuberculosis are usually performed with chemical fixation using glutaraldehyde (GA) in a biosafety area followed by post-fixation with aqueous osmium tetroxide (OT) in a conventional laboratory outside the biosafety area. Freeze-substitution with osmium-acetone (OA) at ultralow temperature (-85°C) has been shown to provide high quality final images and preserves cellular structures intact. However, some preparation procedures for freeze-substitution often require large fixed devices for freezing in a special laboratory. We have reported a novel freeze-substitution preparation method that can be performed using a portable device in a biosafety cabinet at biosafety level (BSL) 3 areas. Here, as a next step, we examined whether images obtained from rapid freeze-substitution (RFS) after fixation with glutaraldehyde (GA>RFS) are of comparable quality to those obtained using standard RFS. GA>RFS provided excellent preservation of mycobacterial cell ultrastructure, including visualization of cytoplasmic ribosomes, DNA fibers, and the outer membrane. The average number of ribosomes per cubic micrometer counted on RFS and GA>RFS was not significantly different (6987.8±2181.0 and 6888.9±1799.3, respectively). These values were higher, but not significantly so, than those obtained using conventional chemical fixation (5018.7±2511.3). This procedure may be useful for RFS preparation of unculturable mycobacteria strains or virulent strains isolated in laboratories that cannot perform RFS.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Akio Aono
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
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22
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Kopecká M, Kawamoto S, Yamaguchi M. A new F-actin structure in fungi: actin ring formation around the cell nucleus of Cryptococcus neoformans. Microscopy (Oxf) 2012; 62:295-301. [PMID: 23155113 DOI: 10.1093/jmicro/dfs074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The F-actin cytoskeleton of Cryptococcus neoformans is known to comprise actin cables, cortical patches and cytokinetic ring. Here, we describe a new F-actin structure in fungi, a perinuclear F-actin collar ring around the cell nucleus, by fluorescent microscopic imaging of rhodamine phalloidin-stained F-actin. Perinuclear F-actin rings form in Cryptococcus neoformans treated with the microtubule inhibitor Nocodazole or with the drug solvent dimethyl sulfoxide (DMSO) or grown in yeast extract peptone dextrose (YEPD) medium, but they are absent in cells treated with Latrunculin A. Perinuclear F-actin rings may function as 'funicular cabin' for the cell nucleus, and actin cables as intracellular 'funicular' suspending nucleus in the central position in the cell and moving nucleus along the polarity axis along actin cables.
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Affiliation(s)
- Marie Kopecká
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 62500, Czech Republic.
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23
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Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K. Prokaryote or eukaryote? A unique microorganism from the deep sea. Microscopy (Oxf) 2012; 61:423-431. [PMID: 23024290 DOI: 10.1093/jmicro/dfs062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
There are only two kinds of organisms on the Earth: prokaryotes and eukaryotes. Although eukaryotes are considered to have evolved from prokaryotes, there were no previously known intermediate forms between them. The differences in their cellular structures are so vast that the problem of how eukaryotes could have evolved from prokaryotes is one of the greatest enigmas in biology. Here, we report a unique organism with cellular structures appearing to have intermediate features between prokaryotes and eukaryotes, which was discovered in the deep sea off the coast of Japan using electron microscopy and structome analysis. The organism was 10 µm long and 3 µm in diameter, having >100 times the volume of Escherichia coli. It had a large 'nucleoid', consisting of naked DNA fibers, with a single nucleoid membrane and endosymbionts that resemble bacteria, but no mitochondria. Because this organism appears to be a life form distinct from both prokaryotes and eukaryotes but similar to eukaryotes, we named this unique microorganism the 'Myojin parakaryote' with the scientific name of Parakaryon myojinensis ('next to (eu)karyote from Myojin') after the discovery location and its intermediate morphology. The existence of this organism is an indication of a potential evolutionary path between prokaryotes and eukaryotes.
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Affiliation(s)
- Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan
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