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Ojima Y, Toda K, Sawabe T, Kumazoe Y, Tahara YO, Miyata M, Azuma M. Budding and explosive membrane vesicle production by hypervesiculating Escherichia coli strain Δ rodZ. Front Microbiol 2024; 15:1400434. [PMID: 38966389 PMCID: PMC11222570 DOI: 10.3389/fmicb.2024.1400434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Escherichia coli produces extracellular vesicles called outer membrane vesicles. In this study, we investigated the mechanism underlying the hypervesiculation of deletion mutant ΔrodZ of E. coli. RodZ forms supramolecular complexes with actin protein MreB and peptidoglycan (PG) synthase, and plays an important role in determining the cell shape. Because mreB is an essential gene, an expression-repressed strain (mreB R3) was constructed using CRISPRi, in which the expression of mreB decreased to 20% of that in the wild-type (WT) strain. In shaken-flask culture, the ΔrodZ strain produced >50 times more vesicles than the WT strain. The mreB-repressed strain mreB R3 showed eightfold higher vesicle production than the WT. ΔrodZ and mreB R3 cells were observed using quick-freeze replica electron microscopy. As reported in previous studies, ΔrodZ cells were spherical (WT cells are rod-shaped). Some ΔrodZ cells (around 7% in total) had aberrant surface structures, such as budding vesicles and dented surfaces, or curved patterns on the surface. Holes in the PG layer and an increased cell volume were observed for ΔrodZ and mreB R3 cells compared with the WT. In conditions of osmotic support using sucrose, the OD660 value of the ΔrodZ strain increased significantly, and vesicle production decreased drastically, compared with those in the absence of sucrose. This study first clarified that vesicle production by the E. coli ΔrodZ strain is promoted by surface budding and a burst of cells that became osmotically sensitive because of their incomplete PG structure.
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Affiliation(s)
- Yoshihiro Ojima
- Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Kaho Toda
- Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Tomomi Sawabe
- Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Yuki Kumazoe
- Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Masayuki Azuma
- Department of Chemistry and Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
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2
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Jalil K, Tahara YO, Miyata M. Visualization of Bacillus subtilis spore structure and germination using quick-freeze deep-etch electron microscopy. Microscopy (Oxf) 2024:dfae023. [PMID: 38819330 DOI: 10.1093/jmicro/dfae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Bacterial spores, known for their complex and resilient structures, have been the focus of visualization using various methodologies. In this study, we applied quick-freeze and replica electron microscopy techniques, allowing observation of Bacillus subtilis spores in high-contrast and three-dimensional detail. This method facilitated visualization of the spore structure with enhanced resolution and provided new insights into the spores and their germination processes. We identified and described five distinct structures: (i) hair-like structures on the spore surface, (ii) spike formation on the surface of lysozyme-treated spores, (iii) the fractured appearance of the spore cortex during germination, (iv) potential connections between small vesicles and the core membrane and (v) the evolving surface structure of nascent vegetative cells during germination.
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Affiliation(s)
- Kiran Jalil
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
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3
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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.
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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
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4
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Ago R, Tahara YO, Yamaguchi H, Saito M, Ito W, Yamasaki K, Kasai T, Okamoto S, Chikada T, Oshima T, Osaka I, Miyata M, Niki H, Shiomi D. Relationship between the Rod complex and peptidoglycan structure in Escherichia coli. Microbiologyopen 2023; 12:e1385. [PMID: 37877652 PMCID: PMC10561026 DOI: 10.1002/mbo3.1385] [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: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Peptidoglycan for elongation in Escherichia coli is synthesized by the Rod complex, which includes RodZ. Although various mutant strains of the Rod complex have been isolated, the relationship between the activity of the Rod complex and the overall physical and chemical structures of the peptidoglycan have not been reported. We constructed a RodZ mutant, termed RMR, and analyzed the growth rate, morphology, and other characteristics of cells producing the Rod complexes containing RMR. The growth and morphology of RMR cells were abnormal, and we isolated suppressor mutants from RMR cells. Most of the suppressor mutations were found in components of the Rod complex, suggesting that these suppressor mutations increase the integrity and/or the activity of the Rod complex. We purified peptidoglycan from wild-type, RMR, and suppressor mutant cells and observed their structures in detail. We found that the peptidoglycan purified from RMR cells had many large holes and different compositions of muropeptides from those of WT cells. The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure to support the mechanical strength of the cell wall.
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Affiliation(s)
- Risa Ago
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Yuhei O. Tahara
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Honoka Yamaguchi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Motoya Saito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Wakana Ito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Kaito Yamasaki
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Taishi Kasai
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Sho Okamoto
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
| | - Taiki Chikada
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Taku Oshima
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Makoto Miyata
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- Department of GeneticsThe Graduate University for Advanced Studies, SOKENDAIMishimaShizuokaJapan
| | - Daisuke Shiomi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
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5
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Tahara YO, Miyata M. Visualization of Peptidoglycan Structures of Escherichia coli by Quick-Freeze Deep-Etch Electron Microscopy. Methods Mol Biol 2023; 2646:299-307. [PMID: 36842124 DOI: 10.1007/978-1-0716-3060-0_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall that protects the cell from turgor pressure and maintains its shape. In diderm (gram-negative) bacteria, such as Escherichia coli, the PG layer is flexible with a thickness of a 2-6 nm, and its visualization is difficult due to the presence of the outer membrane. The quick-freeze deep-etch replica method has been widely used for the visualization of flexible structures in cell interior, such as cell organelles and membrane components. In this technique, a platinum replica on the surface of a specimen fixed by freezing is observed using a transmission electron microscope. In this chapter, we describe the application of this method for visualizing the E. coli PG layer. We expect that these methods will be useful for the visualization of the PG layer in diverse bacterial species.
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Affiliation(s)
- Yuhei O Tahara
- Graduate School of Science, Osaka City University, Osaka, Japan. .,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan. .,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan.
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,Graduate School of Science, Osaka Metropolitan University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
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6
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Liu Y, Chen J, Raj K, Baerg L, Nathan N, Philpott DJ, Mahadevan R. A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses. ACS Synth Biol 2023; 12:319-328. [PMID: 36592614 DOI: 10.1021/acssynbio.2c00583] [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: 01/03/2023]
Abstract
Both Gram-positive and Gram-negative bacteria release nanosized extracellular vesicles called membrane vesicles (MVs, 20-400 nm), which have great potential in various biomedical applications due to their abilities to deliver effector molecules and induce therapeutic responses. To fully utilize bacterial MVs for therapeutic purposes, regulated and enhanced production of MVs would be highly advantageous. In this study, we developed a universal method to enhance MV yields in both G+/G- bacteria through an autonomous controlled peptidoglycan hydrolase (PGase) expression system. A significant increase (9.37-fold) of MV concentration was observed in engineered E. coli Nissle 1917 compared to the wild-type. With the help of this autonomous system, for the first time we experimentally confirmed horizontal gene transfer and nutrient acquisition in a cocultured bacterial consortium. Furthermore, the engineered probiotic E. coli strains with high yield of MVs showed higher activation of the innate immune responses in human embryonic kidney 293T (HEK293T) and human colorectal carcinoma cells (HCT116), thereby demonstrating the great potential of engineering probiotics in immunology and further living therapeutics in humans.
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Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Lauren Baerg
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Nayanan Nathan
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.,Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
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7
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Electrical monitoring of infection biomarkers in chronic wounds using nanochannels. Biosens Bioelectron 2022; 209:114243. [PMID: 35421671 DOI: 10.1016/j.bios.2022.114243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/22/2022]
Abstract
Chronic wounds represent an important healthcare challenge in developed countries, being wound infection a serious complication with significant impact on patients' life conditions. However, there is a lack of methods allowing an early diagnosis of infection and a right decision making for a correct treatment. In this context, we propose a novel methodology for the electrical monitoring of infection biomarkers in chronic wound exudates, using nanoporous alumina membranes. Lysozyme, an enzyme produced by the human immune system indicating wound infection, is selected as a model compound to prove the concept. Peptidoglycan, a component of the bacterial layer and the native substrate of lysozyme, is immobilized on the inner walls of the nanochannels, blocking them both sterically and electrostatically. The steric blocking is dependent on the pore size (20-100 nm) and the peptidoglycan concentration, whereas the electrostatic blocking depends on the pH. The proposed analytical method is based on the electrical monitoring of the steric/electrostatic nanochannels unblocking upon the specific degradation of peptidoglycan by lysozyme, allowing to detect the infection biomarker at 280 ng/mL levels, which are below those expected in wounds. The low protein adsorption rate and thus outstanding filtering properties of the nanoporous alumina membranes allowed us to discriminate wound exudates from patients with both sterile and infected ulcers without any sample pre-treatment usually indispensable in most diagnostic devices for analysis of physiological fluids. Although size and charge effects in nanochannels have been previously approached for biosensing purposes, as far as we know, the use of nanoporous membranes for monitoring enzymatic cleavage processes, leading to analytical systems for the specific detection of the enzymes has not been deeply explored so far. Compared with previously reported methods, our methodology presents the advantages of no need of neither bioreceptors (antibodies or aptamers) nor competitive assays, low matrix effects and quantitative and rapid analysis at the point-of-care, being also of potential application for the determination of other protease biomarkers.
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8
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Sakata KT, Hashii K, Yoshizawa K, Tahara YO, Yae K, Tsuda R, Tanaka N, Maeda T, Miyata M, Tabuchi M. Coordinated regulation of TORC2 signaling by MCC/eisosome-associated proteins, Pil1 and tetraspan membrane proteins during the stress response. Mol Microbiol 2022; 117:1227-1244. [PMID: 35383382 DOI: 10.1111/mmi.14903] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
MCCs are linear invaginations of the yeast plasma membrane that form stable membrane microdomains. Although over 20 proteins are localized in the MCCs, it is not well understood how these proteins coordinately maintain normal MCC function. Pil1 is a core eisosome protein and is responsible for MCC-invaginated structures. In addition, six-tetraspan membrane proteins (6-Tsp) are localized in the MCCs and classified into two families, the Sur7 family and Nce102 family. To understand the coordinated function of these MCC proteins, single and multiple deletion mutants of Pil1 and 6-Tsp were generated and their MCC structure and growth under various stresses were investigated. Genetic interaction analysis revealed that the Sur7 family and Nce102 function in stress tolerance and normal eisosome assembly, respectively, by cooperating with Pil1. To further understand the role of MCCs/eisosomes in stress tolerance, we screened for suppressor mutants using the SDS-sensitive phenotype of pil1Δ 6-tspΔ cells. This revealed that SDS sensitivity is caused by hyperactivation of Tor kinase complex 2 (TORC2)-Ypk1 signaling. Interestingly, inhibition of sphingolipid metabolism, a well-known downstream pathway of TORC2-Ypk1 signaling, did not rescue the SDS-sensitivity of pil1Δ 6-tspΔ cells. These results suggest that Pil1 and 6-Tsp cooperatively regulate TORC2 signaling during the stress response.
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Affiliation(s)
- Ken-Taro Sakata
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Keisuke Hashii
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Koushiro Yoshizawa
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Yuhei O Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Kaori Yae
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ryohei Tsuda
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Naotaka Tanaka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, Japan
| | - Mitsuaki Tabuchi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
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9
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Aktar S, Okamoto Y, Ueno S, Tahara YO, Imaizumi M, Shintani M, Miyata M, Futamata H, Nojiri H, Tashiro Y. Incorporation of Plasmid DNA Into Bacterial Membrane Vesicles by Peptidoglycan Defects in Escherichia coli. Front Microbiol 2021; 12:747606. [PMID: 34912309 PMCID: PMC8667616 DOI: 10.3389/fmicb.2021.747606] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
Membrane vesicles (MVs) are released by various prokaryotes and play a role in the delivery of various cell-cell interaction factors. Recent studies have determined that these vesicles are capable of functioning as mediators of horizontal gene transfer. Outer membrane vesicles (OMVs) are a type of MV that is released by Gram-negative bacteria and primarily composed of outer membrane and periplasm components; however, it remains largely unknown why DNA is contained within OMVs. Our study aimed to understand the mechanism by which DNA that is localized in the cytoplasm is incorporated into OMVs in Gram-negative bacteria. We compared DNA associated with OMVs using Escherichia coli BW25113 cells harboring the non-conjugative, non-mobilized, and high-copy plasmid pUC19 and its hypervesiculating mutants that included ΔnlpI, ΔrseA, and ΔtolA. Plasmid copy per vesicle was increased in OMVs derived from ΔnlpI, in which peptidoglycan (PG) breakdown and synthesis are altered. When supplemented with 1% glycine to inhibit PG synthesis, both OMV formation and plasmid copy per vesicle were increased in the wild type. The bacterial membrane condition test indicated that membrane permeability was increased in the presence of glycine at the late exponential phase, in which cell lysis did not occur. Additionally, quick-freeze deep-etch and replica electron microscopy observations revealed that outer-inner membrane vesicles (O-IMVs) are formed in the presence of glycine. Thus, two proposed routes for DNA incorporation into OMVs under PG-damaged conditions are suggested. These routes include DNA leakage due to increased membrane permeation and O-IMV formation. Additionally, our findings contribute to a greater understanding of the vesicle-mediated horizontal gene transfer that occurs in nature and the utilization of MVs for DNA cargo.
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Affiliation(s)
- Sharmin Aktar
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Yuhi Okamoto
- Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
| | - So Ueno
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | | | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan.,Faculty of Engineering, Shizuoka University, Hamamatsu, Japan.,Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Hiroyuki Futamata
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan.,Faculty of Engineering, Shizuoka University, Hamamatsu, Japan.,Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hideaki Nojiri
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan.,Faculty of Engineering, Shizuoka University, Hamamatsu, Japan.,Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan.,JST PRESTO, Kawaguchi, Japan
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10
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Ojima Y, Sawabe T, Nakagawa M, Tahara YO, Miyata M, Azuma M. Aberrant Membrane Structures in Hypervesiculating Escherichia coli Strain ΔmlaE ΔnlpI Visualized by Electron Microscopy. Front Microbiol 2021; 12:706525. [PMID: 34456889 PMCID: PMC8386018 DOI: 10.3389/fmicb.2021.706525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli produces extracellular vesicles called outer membrane vesicles (OMVs) by releasing a part of its outer membrane. We previously reported that the combined deletion of nlpI and mlaE, related to envelope structure and phospholipid accumulation in the outer leaflet of the outer membrane, respectively, resulted in the synergistic increase of OMV production. In this study, the analysis of ΔmlaEΔnlpI cells using quick-freeze, deep-etch electron microscopy (QFDE-EM) revealed that plasmolysis occurred at the tip of the long axis in cells and that OMVs formed from this tip. Plasmolysis was also observed in the single-gene knockout mutants ΔnlpI and ΔmlaE. This study has demonstrated that plasmolysis was induced in the hypervesiculating mutant E. coli cells. Furthermore, intracellular vesicles and multilamellar OMV were observed in the ΔmlaEΔnlpI cells. Meanwhile, the secretion of recombinant green fluorescent protein (GFP) expressed in the cytosol of the ΔmlaEΔnlpI cells was more than 100 times higher than that of WT and ΔnlpI, and about 50 times higher than that of ΔmlaE in the OMV fraction, suggesting that cytosolic components were incorporated into outer-inner membrane vesicles (OIMVs) and released into the extracellular space. Additionally, QFDE-EM analysis revealed that ΔmlaEΔnlpI sacculi contained many holes noticeably larger than the mean radius of the peptidoglycan (PG) pores in wild-type (WT) E. coli. These results suggest that in ΔmlaEΔnlpI cells, cytoplasmic membrane materials protrude into the periplasmic space through the peptidoglycan holes and are released as OIMVs.
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Affiliation(s)
- Yoshihiro Ojima
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
| | - Tomomi Sawabe
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
| | - Mao Nakagawa
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Masayuki Azuma
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
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11
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Abstract
Mycoplasma mobile, a parasitic bacterium, glides on solid surfaces, such as animal cells and glass, by a special mechanism. This process is driven by the force generated through ATP hydrolysis on an internal structure. However, the spatial and temporal behaviors of the internal structures in living cells are unclear. In this study, we detected the movements of the internal structure by scanning cells immobilized on a glass substrate using high-speed atomic force microscopy (HS-AFM). By scanning the surface of a cell, we succeeded in visualizing particles, 2 nm in height and aligned mostly along the cell axis with a pitch of 31.5 nm, consistent with previously reported features based on electron microscopy. Movements of individual particles were then analyzed by HS-AFM. In the presence of sodium azide, the average speed of particle movements was reduced, suggesting that movement is linked to ATP hydrolysis. Partial inhibition of the reaction by sodium azide enabled us to analyze particle behavior in detail, showing that the particles move 9 nm right, relative to the gliding direction, and 2 nm into the cell interior in 330 ms and then return to their original position, based on ATP hydrolysis.
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12
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Ueda Y, Tahara YO, Miyata M, Ogita A, Yamaguchi Y, Tanaka T, Fujita KI. Involvement of a Multidrug Efflux Pump and Alterations in Cell Surface Structure in the Synergistic Antifungal Activity of Nagilactone E and Anethole against Budding Yeast Saccharomyces cerevisiae. Antibiotics (Basel) 2021; 10:antibiotics10050537. [PMID: 34066540 PMCID: PMC8148520 DOI: 10.3390/antibiotics10050537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022] Open
Abstract
Nagilactone E, an antifungal agent derived from the root bark of Podocarpus nagi, inhibits 1,3-β glucan synthesis; however, its inhibitory activity is weak. Anethole, the principal component of anise oil, enhances the antifungal activity of nagilactone E. We aimed to determine the combinatorial effect and underlying mechanisms of action of nagilactone E and anethole against the budding yeast Saccharomyces cerevisiae. Analyses using gene-deficient strains showed that the multidrug efflux pump PDR5 is associated with nagilactone E resistance; its transcription was gradually restricted in cells treated with the drug combination for a prolonged duration but not in nagilactone-E-treated cells. Green-fluorescent-protein-tagged Pdr5p was intensively expressed and localized on the plasma membrane of nagilactone-E-treated cells but not in drug-combination-treated cells. Quick-freeze deep-etch electron microscopy revealed the smoothening of intertwined fiber structures on the cell surface of drug-combination-treated cells and spheroplasts, indicating a decline in cell wall components and loss of cell wall strength. Anethole enhanced the antifungal activity of nagilactone E by enabling its retention within cells, thereby accelerating cell wall damage. The combination of nagilactone E and anethole can be employed in clinical settings as an antifungal, as well as a food preservative to restrict food spoilage.
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Affiliation(s)
- Yuki Ueda
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Akira Ogita
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
- Research Center for Urban Health and Sports, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yoshihiro Yamaguchi
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Toshio Tanaka
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
| | - Ken-ichi Fujita
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (Y.U.); (Y.O.T.); (M.M.); (A.O.); (Y.Y.); (T.T.)
- Correspondence: ; Tel.: +81-6-6605-2580
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13
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Frederiksen CØ, Cohn MT, Skov LK, Schmidt EGW, Schnorr KM, Buskov S, Leppänen M, Maasilta I, Perez-Calvo E, Lopez-Ulibarri R, Klausen M. A muramidase from Acremonium alcalophilum hydrolyse peptidoglycan found in the gastrointestinal tract of broiler chickens. J Ind Microbiol Biotechnol 2021; 48:6128676. [PMID: 33693885 PMCID: PMC9113140 DOI: 10.1093/jimb/kuab008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022]
Abstract
This study evaluates peptidoglycan hydrolysis by a microbial muramidase from the
fungus Acremonium alcalophilum in vitro and in the
gastrointestinal tract of broiler chickens. Peptidoglycan used for in
vitro studies was derived from 5 gram-positive chicken gut isolate
type strains. In vitro peptidoglycan hydrolysis was studied by
three approaches: (a) helium ion microscopy to identify visual phenotypes of
hydrolysis, (b) reducing end assay to quantify solubilization of peptidoglycan
fragments, and (c) mass spectroscopy to estimate relative abundances of soluble
substrates and reaction products. Visual effects of peptidoglycan hydrolysis
could be observed by helium ion microscopy and the increase in abundance of
soluble peptidoglycan due to hydrolysis was quantified by a reducing end assay.
Mass spectroscopy confirmed the release of hydrolysis products and identified
muropeptides from the five different peptidoglycan sources. Peptidoglycan
hydrolysis in chicken crop, jejunum, and caecum samples was measured by
quantifying the total and soluble muramic acid content. A significant increase
in the proportion of the soluble muramic acid was observed in all three segments
upon inclusion of the microbial muramidase in the diet.
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Affiliation(s)
| | | | | | | | | | | | - Miika Leppänen
- Department of Biological and Environmental Sciences and Department of Physics, University of Jyvaskyla, Jyvaskyla, FI-40014, Finland
| | - Ilari Maasilta
- Department of Physics, University of Jyvaskyla, Jyvaskyla, FI-40014, Finland
| | - Estefania Perez-Calvo
- Research Centre for Animal Nutrition and Health, DSM Nutritional Products, Village-Neuf, F-68305 Saint Louis, France
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14
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New approaches and techniques for bacterial cell wall analysis. Curr Opin Microbiol 2021; 60:88-95. [PMID: 33631455 DOI: 10.1016/j.mib.2021.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022]
Abstract
Peptidoglycan (PG) has remained for decades in the spotlight of the never-ending battle against pathogenic bacteria as this essential bacterial structure is one of the most successful targets for antibiotics. Most of our current understanding about the composition, architecture, and dynamics of the PG relies on techniques which have experienced great technological and methodological improvements in the past years. Here we summarize recent advances in these methods with the intention to furnish a valuable resource for both PG experts and newcomers.
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15
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Mycolic acid-containing bacteria trigger distinct types of membrane vesicles through different routes. iScience 2021; 24:102015. [PMID: 33532712 PMCID: PMC7835258 DOI: 10.1016/j.isci.2020.102015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/20/2020] [Accepted: 12/28/2020] [Indexed: 01/15/2023] Open
Abstract
Bacterial membrane vesicles (MVs) are attracting considerable attention in diverse fields of life science and biotechnology due to their potential for various applications. Although there has been progress in determining the mechanisms of MV formation in Gram-negative and Gram-positive bacteria, the mechanisms in mycolic acid-containing bacteria remain an unsolved question due to its complex cell envelope structure. Here, by adapting super-resolution live-cell imaging and biochemical analysis, we show that Corynebacterium glutamicum form distinct types of MVs via different routes in response to environmental conditions. DNA-damaging stress induced MV formation through prophage-triggered cell lysis, whereas envelope stress induced MV formation through mycomembrane blebbing. The MV formation routes were conserved in other mycolic acid-containing bacteria. Our results show how the complex cell envelope structure intrinsically generates various types of MVs and will advance our knowledge on how different types of MVs can be generated from a single cell organism. Distinct types of MVs are formed in bacteria with complex cell envelopes MVs can be formed from growing and dying cells via different routes Unique multivesicular MVs can be formed The MV formation routes are conserved among several mycolic-acid containing bacteria
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16
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Tahara YO, Miyata M, Nakamura T. Quick-Freeze, Deep-Etch Electron Microscopy Reveals the Characteristic Architecture of the Fission Yeast Spore. J Fungi (Basel) 2020; 7:jof7010007. [PMID: 33375328 PMCID: PMC7823873 DOI: 10.3390/jof7010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/28/2022] Open
Abstract
The spore of the fission yeast Schizosaccharomyces pombe is a dormant cell that is resistant to a variety of environmental stresses. The S. pombe spore is coated by a proteinaceous surface layer, termed the Isp3 layer because it comprises mainly Isp3 protein. Although thin-section electron microscopy and scanning electron microscopy have revealed the fundamental structure of the spore, its architecture remains unclear. Here we visualized S. pombe spores by using a quick-freeze replica electron microscopy (QFDE-EM) at nanometer resolution, which revealed novel characteristic structures. QFDE-EM revealed that the Isp3 layer exists as an interwoven fibrillar layer. On the spore cell membrane, many deep invaginations, which are longer than those on the vegetative cell membrane, are aligned in parallel. We also observed that during spore germination, the cell surface changes from a smooth to a dendritic filamentous structure, the latter being characteristic of vegetative cells. These findings provide significant insight into not only the structural composition of the spore, but also the mechanism underlying the stress response of the cell.
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Affiliation(s)
- Yuhei O. Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan;
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan;
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
- Correspondence: (M.M.); (T.N.)
| | - Taro Nakamura
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan;
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
- Correspondence: (M.M.); (T.N.)
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17
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Zhang B, Teraguchi E, Imada K, Tahara YO, Nakamura S, Miyata M, Kagiwada S, Nakamura T. The Fission Yeast RNA-Binding Protein Meu5 Is Involved in Outer Forespore Membrane Breakdown during Spore Formation. J Fungi (Basel) 2020; 6:jof6040284. [PMID: 33202882 PMCID: PMC7712723 DOI: 10.3390/jof6040284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
In Schizosaccharomyces pombe, the spore wall confers strong resistance against external stress. During meiosis II, the double-layered intracellular forespore membrane (FSM) forms de novo and encapsulates the nucleus. Eventually, the inner FSM layer becomes the plasma membrane of the spore, while the outer layer breaks down. However, the molecular mechanism and biological significance of this membrane breakdown remain unknown. Here, by genetic investigation of an S. pombe mutant (E22) with normal prespore formation but abnormal spores, we showed that Meu5, an RNA-binding protein known to bind to and stabilize more than 80 transcripts, is involved in this process. We confirmed that the E22 mutant does not produce Meu5 protein, while overexpression of meu5+ in E22 restores the sporulation defect. Furthermore, electron microscopy revealed that the outer membrane of the FSM persisted in meu5∆ spores. Investigation of the target genes of meu5+ showed that a mutant of cyc1+ encoding cytochrome c also showed a severe defect in outer FSM breakdown. Lastly, we determined that outer FSM breakdown occurs coincident with or after formation of the outermost Isp3 layer of the spore wall. Collectively, our data provide novel insights into the molecular mechanism of spore formation.
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Affiliation(s)
- Bowen Zhang
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
| | - Erika Teraguchi
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
| | - Kazuki Imada
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- Department of Chemistry and Biochemistry, National Institute of Technology, Suzuka College, Suzuka 510-0294, Japan
| | - Yuhei O. Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shuko Nakamura
- Department of Biological Sciences, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan; (S.N.); (S.K.)
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Satoshi Kagiwada
- Department of Biological Sciences, Faculty of Science, Nara Women’s University, Nara 630-8506, Japan; (S.N.); (S.K.)
| | - Taro Nakamura
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan; (B.Z.); (E.T.); (K.I.); (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
- Correspondence:
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18
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Multilamellar and Multivesicular Outer Membrane Vesicles Produced by a Buttiauxella agrestis tolB Mutant. Appl Environ Microbiol 2020; 86:AEM.01131-20. [PMID: 32801184 DOI: 10.1128/aem.01131-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Outer membrane vesicles (OMVs) are naturally released from Gram-negative bacteria and play important roles in various biological functions. Released vesicles are not uniform in shape, size, or characteristics, and little is known about this diversity of OMVs. Here, we show that deletion of tolB, which encodes a part of the Tol-Pal system, leads to the production of multiple types of vesicles and increases overall vesicle production in the high-vesicle-forming Buttiauxella agrestis type strain JCM 1090. The ΔtolB mutant produced small OMVs and multilamellar/multivesicular OMVs (M-OMVs) as well as vesicles with a striking similarity to the wild type. M-OMVs, previously undescribed, contained triple-lamellar membrane vesicles and multiple vesicle-incorporating vesicles. Ultracentrifugation enabled the separation and purification of each type of OMV released from the ΔtolB mutant, and visualization by quick-freeze deep-etch and replica electron microscopy indicated that M-OMVs are composed of several lamellar membranes. Visualization of intracellular compartments of ΔtolB mutant cells showed that vesicles were accumulated in the broad periplasm, which is probably due to the low linkage between the outer and inner membranes attributed to the Tol-Pal defect. The outer membrane was invaginating inward by wrapping a vesicle, and the precursor of M-OMVs existed in the cell. Thus, we demonstrated a novel type of bacterial OMV and showed that unconventional processes enable the B. agrestis ΔtolB mutant to form unique vesicles.IMPORTANCE Membrane vesicle (MV) formation has been recognized as a common mechanism in prokaryotes, and MVs play critical roles in intercellular interaction. However, a broad range of MV types and their multiple production processes make it difficult to gain a comprehensive understanding of MVs. In this work, using vesicle separation and electron microscopic analyses, we demonstrated that diverse types of outer membrane vesicles (OMVs) were released from an engineered strain, Buttiauxella agrestis JCM 1090T ΔtolB mutant. We also discovered a previously undiscovered type of vesicle, multilamellar/multivesicular outer membrane vesicles (M-OMVs), which were released by this mutant using unconventional processes. These findings have facilitated considerable progress in understanding MV diversity and expanding the utility of MVs in biotechnological applications.
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19
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Miyata M, Robinson RC, Uyeda TQP, Fukumori Y, Fukushima SI, Haruta S, Homma M, Inaba K, Ito M, Kaito C, Kato K, Kenri T, Kinosita Y, Kojima S, Minamino T, Mori H, Nakamura S, Nakane D, Nakayama K, Nishiyama M, Shibata S, Shimabukuro K, Tamakoshi M, Taoka A, Tashiro Y, Tulum I, Wada H, Wakabayashi KI. Tree of motility - A proposed history of motility systems in the tree of life. Genes Cells 2020; 25:6-21. [PMID: 31957229 PMCID: PMC7004002 DOI: 10.1111/gtc.12737] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/27/2022]
Abstract
Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Technology, Waseda University, Tokyo, Japan
| | - Yoshihiro Fukumori
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Tsuyoshi Kenri
- Laboratory of Mycoplasmas and Haemophilus, Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Yamaguchi, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Azuma Taoka
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Isil Tulum
- Department of Botany, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Hirofumi Wada
- Department of Physics, Graduate School of Science and Engineering, Ritsumeikan University, Shiga, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
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20
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Usui Y, Wakabayashi Y, Shimizu T, Tahara YO, Miyata M, Nakamura A, Ito M. A Factor Produced by Kaistia sp. 32K Accelerated the Motility of Methylobacterium sp. ME121. Biomolecules 2020; 10:biom10040618. [PMID: 32316239 PMCID: PMC7226442 DOI: 10.3390/biom10040618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Motile Methylobacterium sp. ME121 and non-motile Kaistia sp. 32K were isolated from the same soil sample. Interestingly, ME121 was significantly more motile in the coculture of ME121 and 32K than in the monoculture of ME121. This advanced motility of ME121 was also observed in the 32K culture supernatant. A swimming acceleration factor, which we named the K factor, was identified in the 32K culture supernatant, purified, characterized as an extracellular polysaccharide (5–10 kDa), and precipitated with 70% ethanol. These results suggest the possibility that the K factor was directly or indirectly sensed by the flagellar stator, accelerating the flagellar rotation of ME121. To the best of our knowledge, no reports describing an acceleration in motility due to coculture with two or more types of bacteria have been published. We propose a mechanism by which the increase in rotational force of the ME121 flagellar motor is caused by the introduction of the additional stator into the motor by the K factor.
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Affiliation(s)
- Yoshiaki Usui
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan; (Y.U.); (Y.W.)
| | - Yuu Wakabayashi
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan; (Y.U.); (Y.W.)
| | - Tetsu Shimizu
- Faculty of Life and Environmental Sciences, and Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; (T.S.); (A.N.)
| | - Yuhei O. Tahara
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka 558-8585, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (Y.O.T.); (M.M.)
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka 558-8585, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, and Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; (T.S.); (A.N.)
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan; (Y.U.); (Y.W.)
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama 350-8585, Japan
- Correspondence: ; Tel.: +81-273-82-9202
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