1
|
Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol 2024; 15:mjad081. [PMID: 38148118 PMCID: PMC11167312 DOI: 10.1093/jmcb/mjad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/02/2022] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.
Collapse
Affiliation(s)
- Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yamazawa
- Advanced Manufacturing Support Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuo Suga
- Multimodal Microstructure Analysis Unit, RIKEN–JEOL Collaboration Center, Kobe 650-0047, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- IFOM—The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
- Osaka Electro-Communication University, Neyagawa 572-8530, Japan
| |
Collapse
|
2
|
Muselikova K, Mouralova K. Synthetic auxin herbicide 2,4-D and its influence on a model BY-2 suspension. Mol Biol Rep 2024; 51:444. [PMID: 38520569 DOI: 10.1007/s11033-024-09392-x] [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: 10/30/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
2,4-D is a broadly used auxin herbicide. The presence of the 2,4-D synthetic auxin in the medium is imperative for long-term BY-2 tobacco suspension viability. The precise mechanism of this symbiosis of the suspension and the synthetic auxin remains unclear. Our goal was to study the hormonal regulation of the growth of the cell suspension; and to describe the experiments clarifying the interaction between the chosen growth regulators and phytohormones on the cellular level, specifically between the 2,4-D synthetic auxin and the native stress phytohormone - ethylene. This study examined the influence of low 2,4-D concentrations stimulating cell growth in vitro as well as the influence of high herbicide concentrations on the model tobacco BY-2 suspension. The culture took 6 days. Different parameters were evaluated, including the influence of different 2,4-D concentrations on the production of the phytohormone ethylene and its precursor 1-Aminocyclopropane-1-carboxylic acid (ACC) in the tobacco cells. The content of 2,4-D in the cells and the medium was established. The observations of the morphological changes showed that a heavy impregnation of the cell walls taking place depending on the concentration of 2,4-D. A dramatic increase in protective polysaccharides and a remodulation of the cell walls by the formation of a pectin shield in artificial conditions were expected and observed. At the same time, massive production of the stress phytohormone ethylene took place, and, because of that, plant mutagenicity, anomalous tumour-type proliferation growth, and the production of supercells were observed. The hypothesis of the protective shield is discussed.
Collapse
Affiliation(s)
- Katerina Muselikova
- Global Change Research Institute, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Katerina Mouralova
- Brno University of Technology, Faculty of Mechanical Engineering, Brno, Czech Republic.
| |
Collapse
|
3
|
Kato S, Tahara YO, Nishimura Y, Uematsu K, Arai T, Nakane D, Ihara A, Nishizaka T, Iwasaki W, Itoh T, Miyata M, Ohkuma M. Cell surface architecture of the cultivated DPANN archaeon Nanobdella aerobiophila. J Bacteriol 2024; 206:e0035123. [PMID: 38289045 PMCID: PMC10882981 DOI: 10.1128/jb.00351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 02/23/2024] Open
Abstract
The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1T and MJ1HA were motile, but sole MJ1T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila.IMPORTANCEDPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
Collapse
Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuki Nishimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Ayaka Ihara
- Department of Physics, Gakushuin University, Tokyo, Japan
| | | | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| |
Collapse
|
4
|
Puzanskiy RK, Romanyuk DA, Kirpichnikova AA, Yemelyanov VV, Shishova MF. Plant Heterotrophic Cultures: No Food, No Growth. PLANTS (BASEL, SWITZERLAND) 2024; 13:277. [PMID: 38256830 PMCID: PMC10821431 DOI: 10.3390/plants13020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.
Collapse
Affiliation(s)
- Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
| | - Daria A. Romanyuk
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia;
| | | | - Vladislav V. Yemelyanov
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.K.); (V.V.Y.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.A.K.); (V.V.Y.)
| |
Collapse
|
5
|
Toyooka K, Goto Y, Hashimoto K, Wakazaki M, Sato M, Hirai MY. Endoplasmic Reticulum Bodies in the Lateral Root Cap Are Involved in the Direct Transport of Beta-Glucosidase to Vacuoles. PLANT & CELL PHYSIOLOGY 2023; 64:461-473. [PMID: 36617247 DOI: 10.1093/pcp/pcac177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 05/17/2023]
Abstract
Programmed cell death (PCD) in lateral root caps (LRCs) is crucial for maintaining root cap functionality. Endoplasmic reticulum (ER) bodies play important roles in plant immunity and PCD. However, the distribution of ER bodies and their communication with vacuoles in the LRC remain elusive. In this study, we investigated the ultrastructure of LRC cells of wild-type and transgenic Arabidopsis lines using an auto-acquisition transmission electron microscope (TEM) system and high-pressure freezing. Gigapixel-scale high-resolution TEM imaging of the transverse and longitudinal sections of roots followed by three-dimensional imaging identified sausage-shaped structures budding from the ER. These were subsequently identified as ER bodies using GFPh transgenic lines expressing green fluorescent protein (GFP) fused with an ER retention signal (HDEL). Immunogold labeling using an anti-GFP antibody detected GFP signals in the ER bodies and vacuoles. The fusion of ER bodies with vacuoles in LRC cells was identified using correlative light and electron microscopy. Imaging of the root tips of a GFPh transgenic line with a PYK10 promoter revealed the localization of PYK10, a member of the β-glucosidase family with an ER retention signal, in the ER bodies in the inner layer along with a fusion of ER bodies with vacuoles in the middle layer and collapse of vacuoles in the outer layer of the LRC. These findings suggest that ER bodies in LRC directly transport β-glucosidases to the vacuoles, and that a subsequent vacuolar collapse triggered by an unknown mechanism releases protective substances to the growing root tip to protect it from the invaders.
Collapse
Affiliation(s)
- Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yumi Goto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Kei Hashimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| |
Collapse
|
6
|
Miyamoto T, Toyooka K, Chuah JA, Odahara M, Higchi-Takeuchi M, Goto Y, Motoda Y, Kigawa T, Kodama Y, Numata K. A Synthetic Multidomain Peptide That Drives a Macropinocytosis-Like Mechanism for Cytosolic Transport of Exogenous Proteins into Plants. JACS AU 2022; 2:223-233. [PMID: 35098239 PMCID: PMC8790739 DOI: 10.1021/jacsau.1c00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 05/28/2023]
Abstract
Direct delivery of proteins into plants represents a promising alternative to conventional gene delivery for probing and modulating cellular functions without the risk of random integration of transgenes into the host genome. This remains challenging, however, because of the lack of a protein delivery tool applicable to diverse plant species and the limited information about the entry mechanisms of exogenous proteins in plant cells. Here, we present the synthetic multidomain peptide (named dTat-Sar-EED4) for cytosolic protein delivery in various plant species via simple peptide-protein coincubation. dTat-Sar-EED4 enabled the cytosolic delivery of an active enzyme with up to ∼20-fold greater efficiency than previously described cell-penetrating peptides in several model plant systems. Our analyses using pharmacological inhibitors and transmission electron microscopy revealed that dTat-Sar-EED4 triggered a unique endocytic mechanism for cargo protein internalization. This endocytic mechanism shares several features with macropinocytosis, including the dependency of actin polymerization, sensitivity to phosphatidylinositol-3 kinase activity, and formation of membrane protrusions and large intracellular vesicles (>200 nm in diameter), even though macropinocytosis has not been identified to date in plants. Our study thus presents a robust molecular tool that can induce a unique cellular uptake mechanism for the efficient transport of bioactive proteins into plants.
Collapse
Affiliation(s)
- Takaaki Miyamoto
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Kiminori Toyooka
- Technology
Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center
for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Jo-Ann Chuah
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Masaki Odahara
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Mieko Higchi-Takeuchi
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Yumi Goto
- Technology
Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center
for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Yoko Motoda
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
- Laboratory
for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics
Research, Yokohama 230-0045, Japan
| | - Takanori Kigawa
- Laboratory
for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics
Research, Yokohama 230-0045, Japan
| | - Yutaka Kodama
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
- Center
for Bioscience Research and Education, Utsunomiya
University, Tochigi 321-8505, Japan
| | - Keiji Numata
- Biomacromolecules
Research Team, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| |
Collapse
|
7
|
Oda Y, Asatsuma S, Nakasone H, Matsuoka K. Sucrose starvation induces the degradation of proteins in trans-Golgi network and secretory vesicle cluster in tobacco BY-2 cells. Biosci Biotechnol Biochem 2020; 84:1652-1666. [PMID: 32338160 DOI: 10.1080/09168451.2020.1756736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
Endomembrane transport system begins at the endoplasmic reticulum (ER), continues to the Golgi apparatus and subsequent compartment called trans-Golgi network (TGN). We found that SUT2, a tobacco sucrose-transporter ortholog and was localized in the TGN, decreased significantly under a sucrose-starvation condition. The tobacco SNARE protein SYP41, localized in the TGN and secretory vesicle cluster (SVC), also decreased under the starvation. Similarly, the SCAMP2-RFP fusion protein, which is localized in TGN, SVC, and plasma membrane (PM), was distributed solely in the PM under the starvation. Under the same starvation condition, protein secretion was not arrested but pectin deposition to cell wall was suppressed. These data indicated that the protein composition in TGN and existence of the SVC are regulated by sugar availability. Furthermore, our findings as well as the involvement of SVC in pectin secretion suggested that synthesis and transport of pectin are regulated by the level of extracellular sugars. ABBREVIATIONS ER: endoplasmic reticulum; GI-TGN: Golgi-released independent TGN; GFP: green fluorescent protein; mRFP: monomeric red fluorescent protein; P4H1.1: prolyl 4-hydroxylase 1.1; PM: plasma membrane; SCAMP2: secretory carrier membrane protein 2; SUT2: sucrose transporter 2; SVC: secretory vesicle cluster; SYP41: syntaxin of plant 41; TGN: trans-Golgi network; YFP: yellow fluorescent protein.
Collapse
Affiliation(s)
- Yamato Oda
- Department of Bioscience and Biotechnology, Graduate School of Bioenvironmental Sciences, Kyushu University , Fukuoka, Japan
| | - Satoru Asatsuma
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University , Fukuoka, Japan
- RIKEN Plant Science Center , Yokohama, Japan
| | - Hiroaki Nakasone
- Department of Bioscience and Biotechnology, Graduate School of Bioenvironmental Sciences, Kyushu University , Fukuoka, Japan
| | - Ken Matsuoka
- Department of Bioscience and Biotechnology, Graduate School of Bioenvironmental Sciences, Kyushu University , Fukuoka, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University , Fukuoka, Japan
- RIKEN Plant Science Center , Yokohama, Japan
| |
Collapse
|
8
|
Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 2020; 577:519-525. [PMID: 31942073 PMCID: PMC7015854 DOI: 10.1038/s41586-019-1916-6] [Citation(s) in RCA: 336] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022]
Abstract
The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.
Collapse
Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Nozomi Nakahara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshinori Takano
- Biogeochemistry Program, Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Katsuyuki Uematsu
- Department of Marine and Earth Sciences, Marine Work Japan, Yokosuka, Japan
| | - Tetsuro Ikuta
- Research Institute for Global Change, JAMSTEC, Yokosuka, Japan
| | - Motoo Ito
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Yohei Matsui
- Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Japan
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuko Yamanaka
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
| |
Collapse
|
9
|
Chen C, Linse K, Uematsu K, Sigwart JD. Cryptic niche switching in a chemosymbiotic gastropod. Proc Biol Sci 2018; 285:20181099. [PMID: 30051825 PMCID: PMC6053925 DOI: 10.1098/rspb.2018.1099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/15/2018] [Indexed: 12/25/2022] Open
Abstract
Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. 'Metamorphosis' broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoing one or more metamorphic transformations before settling into a permanent, adult morphology on the benthos. Post-settlement, the hydrothermal vent gastropod Gigantopelta chessoia experiences a further, cryptic metamorphosis at body sizes around 5-7 mm. The terminal adult stage is entirely dependent on chemoautotrophic symbionts; smaller individuals do not house symbionts and presumably depend on grazing. Using high-resolution X-ray microtomography to reconstruct the internal organs in a growth series, we show that this sudden transition in small but sexually mature individuals dramatically reconfigures the organs, but is in no way apparent from external morphology. We introduce the term 'cryptometamorphosis' to identify this novel phenomenon of a major body change and trophic shift, not related to sexual maturity, transforming only the internal anatomy. Understanding energy flow in ecosystems depends on the feeding ecology of species; the present study highlights the possibility for adult animals to make profound shifts in biology that influence energy dynamics.
Collapse
Affiliation(s)
- Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 2370061, Japan
| | - Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, Kanagawa 2370063, Japan
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry BT22 1PF, N. Ireland
- Museum of Paleontology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
10
|
Meents MJ, Watanabe Y, Samuels AL. The cell biology of secondary cell wall biosynthesis. ANNALS OF BOTANY 2018; 121:1107-1125. [PMID: 29415210 PMCID: PMC5946954 DOI: 10.1093/aob/mcy005] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/16/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Secondary cell walls (SCWs) form the architecture of terrestrial plant biomass. They reinforce tracheary elements and strengthen fibres to permit upright growth and the formation of forest canopies. The cells that synthesize a strong, thick SCW around their protoplast must undergo a dramatic commitment to cellulose, hemicellulose and lignin production. SCOPE This review puts SCW biosynthesis in a cellular context, with the aim of integrating molecular biology and biochemistry with plant cell biology. While SCWs are deposited in diverse tissue and cellular contexts including in sclerenchyma (fibres and sclereids), phloem (fibres) and xylem (tracheids, fibres and vessels), the focus of this review reflects the fact that protoxylem tracheary elements have proven to be the most amenable experimental system in which to study the cell biology of SCWs. CONCLUSIONS SCW biosynthesis requires the co-ordination of plasma membrane cellulose synthases, hemicellulose production in the Golgi and lignin polymer deposition in the apoplast. At the plasma membrane where the SCW is deposited under the guidance of cortical microtubules, there is a high density of SCW cellulose synthase complexes producing cellulose microfibrils consisting of 18-24 glucan chains. These microfibrils are extruded into a cell wall matrix rich in SCW-specific hemicelluloses, typically xylan and mannan. The biosynthesis of eudicot SCW glucuronoxylan is taken as an example to illustrate the emerging importance of protein-protein complexes in the Golgi. From the trans-Golgi, trafficking of vesicles carrying hemicelluloses, cellulose synthases and oxidative enzymes is crucial for exocytosis of SCW components at the microtubule-rich cell membrane domains, producing characteristic SCW patterns. The final step of SCW biosynthesis is lignification, with monolignols secreted by the lignifying cell and, in some cases, by neighbouring cells as well. Oxidative enzymes such as laccases and peroxidases, embedded in the polysaccharide cell wall matrix, determine where lignin is deposited.
Collapse
Affiliation(s)
- Miranda J Meents
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Yoichiro Watanabe
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | |
Collapse
|
11
|
Akita K, Kobayashi M, Sato M, Kutsuna N, Ueda T, Toyooka K, Nagata N, Hasezawa S, Higaki T. Cell wall accumulation of fluorescent proteins derived from a trans-Golgi cisternal membrane marker and paramural bodies in interdigitated Arabidopsis leaf epidermal cells. PROTOPLASMA 2017; 254:367-377. [PMID: 26960821 DOI: 10.1007/s00709-016-0955-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
In most dicotyledonous plants, leaf epidermal pavement cells develop jigsaw puzzle-like shapes during cell expansion. The rapid growth and complicated cell shape of pavement cells is suggested to be achieved by targeted exocytosis that is coordinated with cytoskeletal rearrangement to provide plasma membrane and/or cell wall materials for lobe development during their morphogenesis. Therefore, visualization of membrane trafficking in leaf pavement cells should contribute an understanding of the mechanism of plant cell morphogenesis. To reveal membrane trafficking in pavement cells, we observed monomeric red fluorescent protein-tagged rat sialyl transferases, which are markers of trans-Golgi cisternal membranes, in the leaf epidermis of Arabidopsis thaliana. Quantitative fluorescence imaging techniques and immunoelectron microscopic observations revealed that accumulation of the red fluorescent protein occurred mostly in the curved regions of pavement cell borders and guard cell ends during leaf expansion. Transmission electron microscopy observations revealed that apoplastic vesicular membrane structures called paramural bodies were more frequent beneath the curved cell wall regions of interdigitated pavement cells and guard cell ends in young leaf epidermis. In addition, pharmacological studies showed that perturbations in membrane trafficking resulted in simple cell shapes. These results suggested possible heterogeneity of the curved regions of plasma membranes, implying a relationship with pavement cell morphogenesis.
Collapse
Affiliation(s)
- Kae Akita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Megumi Kobayashi
- Faculty of Science, Japan Women's University, Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Natsumaro Kutsuna
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- Research and Development Division, LPixel Inc., Bunkyo-ku, Tokyo, 150-0002, Japan
| | - Takashi Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Noriko Nagata
- Faculty of Science, Japan Women's University, Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Seiichiro Hasezawa
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Takumi Higaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| |
Collapse
|
12
|
Toyooka K. OB-III-1Development of wide-range and high-resolution transmission electron microscope acquisition system and correlative light & electron microscope system: Applications for ultrastructural analyses of intracellular compartments and trafficking pathways in plant growth and development. Microscopy (Oxf) 2016. [DOI: 10.1093/jmicro/dfw048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
13
|
Uemura T. Physiological Roles of Plant Post-Golgi Transport Pathways in Membrane Trafficking. PLANT & CELL PHYSIOLOGY 2016; 57:2013-2019. [PMID: 27649735 DOI: 10.1093/pcp/pcw149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/12/2016] [Indexed: 05/02/2023]
Abstract
Membrane trafficking is the fundamental system through which proteins are sorted to their correct destinations in eukaryotic cells. Key regulators of this system include RAB GTPases and soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs). Interestingly, the numbers of RAB GTPases and SNAREs involved in post-Golgi transport pathways in plant cells are larger than those in animal and yeast cells, suggesting that plants have evolved unique and complex post-Golgi transport pathways. The trans-Golgi network (TGN) is an important organelle that acts as a sorting station in the post-Golgi transport pathways of plant cells. The TGN also functions as the early endosome, which is the first compartment to receive endocytosed proteins. Several endocytosed proteins on the plasma membrane (PM) are initially targeted to the TGN/EE, then recycled back to the PM or transported to the vacuole for degradation. The recycling and degradation of the PM localized proteins is essential for the development and environmental responses in plant. The present review describes the post-Golgi transport pathways that show unique physiological functions in plants.
Collapse
Affiliation(s)
- Tomohiro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
14
|
Toyooka K, Sato M, Wakazaki M, Matsuoka K. Morphological and quantitative changes in mitochondria, plastids, and peroxisomes during the log-to-stationary transition of the growth phase in cultured tobacco BY-2 cells. PLANT SIGNALING & BEHAVIOR 2016; 11:e1149669. [PMID: 26855065 PMCID: PMC4883831 DOI: 10.1080/15592324.2016.1149669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
We developed a wide-range and high-resolution transmission electron microscope acquisition system and obtained giga-pixel images of tobacco BY-2 cells during the log and stationary phases of cell growth. We demonstrated that the distribution and ultrastructure of compartments involved in membrane traffic (i.e., Golgi apparatus, multivesicular body, and vesicle cluster) change during the log-to-stationary transition. Mitochondria, peroxisomes, and plastids were also enumerated. Electron densities of mitochondria and peroxisomes were altered during the growth-phase shift, while their numbers were reduced by nearly half. Plastid structure dramatically changed from atypical to spherical with starch granules. Nearly the same number of plastids was observed in both log and stationary phases. These results indicate that mechanisms regulating organelle populations differ from organelle to organelle.
Collapse
Affiliation(s)
- Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Ken Matsuoka
- Laboratory of Plant Nutrition, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| |
Collapse
|
15
|
Toyooka K, Hashimoto K, Narikawa N, Wakazaki M, Sato M, Nagata N, Okamoto T. C2-P-02The ER body in the lateral root cap is involved in mass transport of (K/H)DEL proteins to the vacuole: Using Gigapixel TEM images. Microscopy (Oxf) 2015. [DOI: 10.1093/jmicro/dfv298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
16
|
Higaki T, Kutsuna N, Akita K, Sato M, Sawaki F, Kobayashi M, Nagata N, Toyooka K, Hasezawa S. Semi-automatic organelle detection on transmission electron microscopic images. Sci Rep 2015; 5:7794. [PMID: 25589024 PMCID: PMC4295107 DOI: 10.1038/srep07794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/16/2014] [Indexed: 12/17/2022] Open
Abstract
Recent advances in the acquisition of large-scale datasets of transmission electron microscope images have allowed researchers to determine the number and the distribution of subcellular ultrastructures at both the cellular level and the tissue level. For this purpose, it would be very useful to have a computer-assisted system to detect the structures of interest, such as organelles. Using our original image recognition framework CARTA (Clustering-Aided Rapid Training Agent), combined with procedures to highlight and enlarge regions of interest on the image, we have developed a successful method for the semi-automatic detection of plant organelles including mitochondria, amyloplasts, chloroplasts, etioplasts, and Golgi stacks in transmission electron microscope images. Our proposed semi-automatic detection system will be helpful for labelling organelles in the interpretation and/or quantitative analysis of large-scale electron microscope imaging data.
Collapse
Affiliation(s)
- Takumi Higaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa 277-8562, Japan
| | - Natsumaro Kutsuna
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa 277-8562, Japan
- Research and Development Division, LPixel Inc., Bunkyo-ku, Tokyo 150-0002, Japan
| | - Kae Akita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa 277-8562, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Fumie Sawaki
- Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Megumi Kobayashi
- Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Noriko Nagata
- Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Seiichiro Hasezawa
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa 277-8562, Japan
| |
Collapse
|