1
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Skates E, Delattre H, Schofield Z, Asally M, Soyer OS. Thioflavin T indicates mitochondrial membrane potential in mammalian cells. Biophys Rep (N Y) 2023; 3:100134. [PMID: 38026684 PMCID: PMC10679866 DOI: 10.1016/j.bpr.2023.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
The fluorescent benzothiazole dye thioflavin T (ThT) is widely used as a marker for protein aggregates, most commonly in the context of neurodegenerative disease research and diagnosis. Recently, this same dye was shown to indicate membrane potential in bacteria due to its cationic nature. This finding prompted a question whether ThT fluorescence is linked to the membrane potential in mammalian cells, which would be important for appropriate utilization of ThT in research and diagnosis. Here, we show that ThT localizes into the mitochondria of HeLa cells in a membrane-potential-dependent manner. Specifically, ThT colocalized in cells with the mitochondrial membrane potential indicator tetramethylrhodamine methyl ester (TMRM) and gave similar temporal responses as TMRM to treatment with a protonophore, carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP). Additionally, we found that presence of ThT together with exposure to blue light (λ = 405 nm), but neither factor alone, caused depolarization of mitochondrial membrane potential. This additive effect of the concentration and blue light was recapitulated by a mathematical model implementing the potential-dependent distribution of ThT and its effect on mitochondrial membrane potential through photosensitization. These results show that ThT can act as a mitochondrial membrane potential indicator in mammalian cells, when used at low concentrations and with low blue light exposure. However, it causes dissipation of the mitochondrial membrane potential depending additively on its concentrations and blue light exposure. This conclusion motivates a re-evaluation of ThT's use at micromolar range in live-cell analyses and indicates that this dye can enable future studies on the potential connections between mitochondrial membrane potential dynamics and protein aggregation.
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Affiliation(s)
- Emily Skates
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
- Midlands Integrative Doctoral Training Program; University of Warwick, Coventry, United Kingdom
| | - Hadrien Delattre
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Zoe Schofield
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| | - Orkun S. Soyer
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
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2
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Oka M, Otani M, Miyamoto Y, Oshima R, Adachi J, Tomonaga T, Asally M, Nagaoka Y, Tanaka K, Toyoda A, Ichikawa K, Morishita S, Isono K, Koseki H, Nakato R, Ohkawa Y, Yoneda Y. Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure. Cell Rep 2023; 42:112884. [PMID: 37516964 DOI: 10.1016/j.celrep.2023.112884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/29/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies' function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with MLL1/CRM1 and co-localized on chromatin. Furthermore, whole-genome chromatin-conformation capture analysis reveals that NUP98::HOXA9 induces a drastic alteration in high-order genome structure at target regions concomitant with the generation of chromatin loops and/or rearrangement of topologically associating domains in a phase-separation-dependent manner. Collectively, these results show that the phase-separated nuclear bodies of nucleoporin fusion proteins can enhance the activation of target genes by promoting the condensation of MLL1/CRM1 and rearrangement of the 3D genome structure.
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Affiliation(s)
- Masahiro Oka
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Laboratory of Biomedical Innovation, Graduate School of Pharmaceutical Sciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Mayumi Otani
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Rieko Oshima
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteomics for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Munehiro Asally
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Yuya Nagaoka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan
| | - Kyoichi Isono
- Laboratory Animal Center, Wakayama Medical University, 811-1 Kimi-idera, Wakayama 641-8509, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.
| | - Yoshihiro Yoneda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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3
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de Souza‐Guerreiro TC, Bondelli G, Grobas I, Donini S, Sesti V, Bertarelli C, Lanzani G, Asally M, Paternò GM. Membrane Targeted Azobenzene Drives Optical Modulation of Bacterial Membrane Potential. Adv Sci (Weinh) 2023; 10:e2205007. [PMID: 36710255 PMCID: PMC10015841 DOI: 10.1002/advs.202205007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/17/2023] [Indexed: 05/29/2023]
Abstract
Recent studies have shown that bacterial membrane potential is dynamic and plays signaling roles. Yet, little is still known about the mechanisms of membrane potential dynamics regulation-owing to a scarcity of appropriate research tools. Optical modulation of bacterial membrane potential could fill this gap and provide a new approach for studying and controlling bacterial physiology and electrical signaling. Here, the authors show that a membrane-targeted azobenzene (Ziapin2) can be used to photo-modulate the membrane potential in cells of the Gram-positive bacterium Bacillus subtilis. It is found that upon exposure to blue-green light (λ = 470 nm), isomerization of Ziapin2 in the bacteria membrane induces hyperpolarization of the potential. To investigate the origin of this phenomenon, ion-channel-deletion strains and ion channel blockers are examined. The authors found that in presence of the chloride channel blocker idanyloxyacetic acid-94 (IAA-94) or in absence of KtrAB potassium transporter, the hyperpolarization response is attenuated. These results reveal that the Ziapin2 isomerization can induce ion channel opening in the bacterial membrane and suggest that Ziapin2 can be used for studying and controlling bacterial electrical signaling. This new optical tool could contribute to better understand various microbial phenomena, such as biofilm electric signaling and antimicrobial resistance.
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Affiliation(s)
| | - Gaia Bondelli
- Center for Nanoscience and TechnologyIstituto Italiano di TeconologiaMilano20133Italy
| | - Iago Grobas
- Physical and Theoretical Chemistry LaboratoryOxfordOX1 3QZUK
| | - Stefano Donini
- Center for Nanoscience and TechnologyIstituto Italiano di TeconologiaMilano20133Italy
| | - Valentina Sesti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta” Politecnico di MilanoMilano20133Italy
| | - Chiara Bertarelli
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta” Politecnico di MilanoMilano20133Italy
| | - Guglielmo Lanzani
- Center for Nanoscience and TechnologyIstituto Italiano di TeconologiaMilano20133Italy
- Department of PhysicsPolitecnico di MilanoMilano20133Italy
| | - Munehiro Asally
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Giuseppe Maria Paternò
- Center for Nanoscience and TechnologyIstituto Italiano di TeconologiaMilano20133Italy
- Department of PhysicsPolitecnico di MilanoMilano20133Italy
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4
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Back O, Asally M, Wang Z, Hayashi Y. Electrotaxis behavior of droplets composed of aqueous Belousov-Zhabotinsky solutions suspended in oil phase. Sci Rep 2023; 13:1340. [PMID: 36693937 PMCID: PMC9873656 DOI: 10.1038/s41598-023-27639-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Taxis is ubiquitous in biological and physical chemistry systems as a response to various external stimulations. We prepared aqueous droplets containing Belousov-Zhabotinsky (BZ) solutions suspended on an oleic acid oil phase subject to DC electric field and found that these BZ droplets undergo chemically driven translational motion towards the negative electrode under DC electric field. This electrotaxis phenomenon originates from the field-induced inhomogeneous distribution of reactants, in particular Br[Formula: see text] ions, and consequently the biased location of the leading centers towards the positive electrode. We define the 'leading center' (LC) as a specific location within the droplet where the BZ chemical wave (target pattern) is initiated. The chemical wave generated from the LC propagates passing the droplet center of mass and creates a gradient of interfacial tension when reaching the droplet-oil interface on the other side, resulting in a momentum exchange between the droplet and oil phases which drives the droplet motion in the direction of the electric field. A greater electric field strength renders a more substantial electrotaxis effect.
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Affiliation(s)
- Oliver Back
- Department of Biomedical Sciences and Biomedical Engineering, School of Biological Sciences, University of Reading, Reading, UK
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Zuowei Wang
- Department of Mathematics and Statistics, School of Mathematical, Physical and Computational Sciences, University of Reading, Reading, UK
| | - Yoshikatsu Hayashi
- Department of Biomedical Sciences and Biomedical Engineering, School of Biological Sciences, University of Reading, Reading, UK.
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5
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de Souza-Guerreiro TC, Asally M. Seeking Insights into Aging Through Yeast Mitochondrial Electrophysiology. Bioelectricity 2021; 3:111-115. [PMID: 34476385 DOI: 10.1089/bioe.2021.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During aging, mitochondrial membrane potential, a key indicator for bioenergetics of cells, depolarizes in a wide range of species-from yeasts, plants to animals. In humans, the decline of mitochondrial activities can impact the high-energy-consuming organs, such as the brain and heart, and increase the risks of age-linked diseases. Intriguingly, a mild depolarization of mitochondria has lifespan-extending effects, suggesting an important role played by bioelectricity during aging. However, the underpinning biophysical mechanism is not very well understood due in part to the difficulties associated with a multiscale process. Budding yeast Saccharomyces cerevisiae could provide a model system to bridge this knowledge gap and provide insights into aging. In this perspective, we overview recent studies on the yeast mitochondrial membrane electrophysiology and aging and call for more electrochemical and biophysical studies on aging.
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Affiliation(s)
- Tailise Carolina de Souza-Guerreiro
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Munehiro Asally
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom.,School of Life Sciences, University of Warwick, Coventry, United Kingdom.,Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
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6
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Asally M, Prindle A. Microbial Electrophysiology. Bioelectricity 2021; 3:110. [PMID: 34476384 DOI: 10.1089/bioe.2021.0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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7
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Grobas I, Polin M, Asally M. Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms. eLife 2021; 10:62632. [PMID: 33722344 PMCID: PMC7963483 DOI: 10.7554/elife.62632] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/26/2021] [Indexed: 12/23/2022] Open
Abstract
Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.
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Affiliation(s)
- Iago Grobas
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom
| | - Marco Polin
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom.,Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, United Kingdom.,Physics Department, University of Warwick, Coventry, United Kingdom.,Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), C/ Miquel Marqués, Balearic Islands, Spain
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
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8
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Kano T, Yasui K, Mikami T, Asally M, Ishiguro A. An agent-based model of the interrelation between the COVID-19 outbreak and economic activities. Proc Math Phys Eng Sci 2021; 477:20200604. [PMID: 33633491 PMCID: PMC7897648 DOI: 10.1098/rspa.2020.0604] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 01/19/2023] Open
Abstract
As of July 2020, COVID-19 caused by SARS-COV-2 is spreading worldwide, causing severe economic damage. While minimizing human contact is effective in managing outbreaks, it causes severe economic losses. Strategies to solve this dilemma by considering the interrelation between the spread of the virus and economic activities are urgently needed to mitigate the health and economic damage. Here, we propose an abstract agent-based model of the COVID-19 outbreak that accounts for economic activities. The computational simulation of the model recapitulates the trade-off between the health and economic damage associated with voluntary restraint measures. Based on the simulation results, we discuss how the macroscopic dynamics of infection and economics emerge from individuals' behaviours. We believe our model can serve as a platform for discussing solutions to the above-mentioned dilemma.
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Affiliation(s)
- Takeshi Kano
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8578, Japan
| | - Kotaro Yasui
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8578, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki aza Aoba 6-3, Aoba-ku, Sendai 980-8578, Japan
| | - Taishi Mikami
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8578, Japan
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
| | - Akio Ishiguro
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8578, Japan
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9
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Grobas I, Bazzoli DG, Asally M. Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools. Biochem Soc Trans 2020; 48:2903-2913. [PMID: 33300966 PMCID: PMC7752047 DOI: 10.1042/bst20200972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell-cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.
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Affiliation(s)
- Iago Grobas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Dario G. Bazzoli
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, U.K
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K
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10
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Cremin K, Jones BA, Teahan J, Meloni GN, Perry D, Zerfass C, Asally M, Soyer OS, Unwin PR. Scanning Ion Conductance Microscopy Reveals Differences in the Ionic Environments of Gram-Positive and Negative Bacteria. Anal Chem 2020; 92:16024-16032. [PMID: 33241929 DOI: 10.1021/acs.analchem.0c03653] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This paper reports on the use of scanning ion conductance microscopy (SICM) to locally map the ionic properties and charge environment of two live bacterial strains: the Gram-negative Escherichia coli and the Gram-positive Bacillus subtilis. SICM results find heterogeneities across the bacterial surface and significant differences among the Gram-positive and Gram-negative bacteria. The bioelectrical environment of the B. subtilis was found to be considerably more negatively charged compared to E. coli. SICM measurements, fitted to a simplified finite element method (FEM) model, revealed surface charge values of -80 to -140 mC m-2 for the Gram-negative E. coli. The Gram-positive B. subtilis show a much higher conductivity around the cell wall, and surface charge values between -350 and -450 mC m-2 were found using the same simplified model. SICM was also able to detect regions of high negative charge near B. subtilis, not detected in the topographical SICM response and attributed to the extracellular polymeric substance. To further explore how the B. subtilis cell wall structure can influence the SICM current response, a more comprehensive FEM model, accounting for the physical properties of the Gram-positive cell wall, was developed. The new model provides a more realistic description of the cell wall and allows investigation of the relation between its key properties and SICM currents, building foundations to further investigate and improve understanding of the Gram-positive cellular microenvironment.
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Affiliation(s)
- Kelsey Cremin
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,Molecular Analytical Science Centre for Doctoral Training (MAS CDT), University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Bryn A Jones
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - James Teahan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,Molecular Analytical Science Centre for Doctoral Training (MAS CDT), University of Warwick, Coventry CV4 7AL, U.K
| | - Gabriel N Meloni
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - David Perry
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Christian Zerfass
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Orkun S Soyer
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Patrick R Unwin
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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11
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Kantsler V, Ontañón-McDonald E, Kuey C, Ghanshyam MJ, Roffin MC, Asally M. Correction to "Pattern Engineering of Living Bacterial Colonies Using Meniscus-Driven Fluidic Channels". ACS Synth Biol 2020; 9:2616. [PMID: 32790280 DOI: 10.1021/acssynbio.0c00381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Kantsler V, Ontañón-McDonald E, Kuey C, Ghanshyam MJ, Roffin MC, Asally M. Pattern Engineering of Living Bacterial Colonies Using Meniscus-Driven Fluidic Channels. ACS Synth Biol 2020; 9:1277-1283. [PMID: 32491836 DOI: 10.1021/acssynbio.0c00146] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Creating adaptive, sustainable, and dynamic biomaterials is a forthcoming mission of synthetic biology. Engineering spatially organized bacterial communities has a potential to develop such bio-metamaterials. However, generating living patterns with precision, robustness, and a low technical barrier remains as a challenge. Here we present an easily implementable technique for patterning live bacterial populations using a controlled meniscus-driven fluidics system, named as MeniFluidics. We demonstrate multiscale patterning of biofilm colonies and swarms with submillimeter resolution. Utilizing the faster bacterial spreading in liquid channels, MeniFluidics allows controlled bacterial colonies both in space and time to organize fluorescently labeled Bacillus subtilis strains into a converged pattern and to form dynamic vortex patterns in confined bacterial swarms. The robustness, accuracy, and low technical barrier of MeniFluidics offer a tool for advancing and inventing new living materials that can be combined with genetically engineered systems, and adding to fundamental research into ecological, evolutional, and physical interactions between microbes.
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Affiliation(s)
- Vasily Kantsler
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Cansu Kuey
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Manjari J. Ghanshyam
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Maria Chiara Roffin
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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13
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Schofield Z, Meloni GN, Tran P, Zerfass C, Sena G, Hayashi Y, Grant M, Contera SA, Minteer SD, Kim M, Prindle A, Rocha PRF, Djamgoz MBA, Pilizota T, Unwin PR, Asally M, Soyer OS. Correction to 'Bioelectrical understanding and engineering of cell biology'. J R Soc Interface 2020; 17:20200435. [PMID: 32546111 DOI: 10.1098/rsif.2020.0435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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14
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Schofield Z, Meloni GN, Tran P, Zerfass C, Sena G, Hayashi Y, Grant M, Contera SA, Minteer SD, Kim M, Prindle A, Rocha P, Djamgoz MBA, Pilizota T, Unwin PR, Asally M, Soyer OS. Bioelectrical understanding and engineering of cell biology. J R Soc Interface 2020; 17:20200013. [PMID: 32429828 PMCID: PMC7276535 DOI: 10.1098/rsif.2020.0013] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
The last five decades of molecular and systems biology research have provided unprecedented insights into the molecular and genetic basis of many cellular processes. Despite these insights, however, it is arguable that there is still only limited predictive understanding of cell behaviours. In particular, the basis of heterogeneity in single-cell behaviour and the initiation of many different metabolic, transcriptional or mechanical responses to environmental stimuli remain largely unexplained. To go beyond the status quo, the understanding of cell behaviours emerging from molecular genetics must be complemented with physical and physiological ones, focusing on the intracellular and extracellular conditions within and around cells. Here, we argue that such a combination of genetics, physics and physiology can be grounded on a bioelectrical conceptualization of cells. We motivate the reasoning behind such a proposal and describe examples where a bioelectrical view has been shown to, or can, provide predictive biological understanding. In addition, we discuss how this view opens up novel ways to control cell behaviours by electrical and electrochemical means, setting the stage for the emergence of bioelectrical engineering.
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Affiliation(s)
- Zoe Schofield
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Gabriel N. Meloni
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Peter Tran
- Department of Chemical and Biological Engineering, Northwestern University, Chicago, IL 60611, USA
| | - Christian Zerfass
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Giovanni Sena
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Yoshikatsu Hayashi
- Department of Biomedical Engineering, School of Biological Sciences, University of Reading, Reading RG6 6AH, UK
| | - Murray Grant
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sonia A. Contera
- Clarendon Laboratory, Physics Department, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | - Arthur Prindle
- Department of Chemical and Biological Engineering, Northwestern University, Chicago, IL 60611, USA
| | - Paulo Rocha
- Centre for Biosensors, Bioelectronics and Biodevices (C3Bio), Department of Electronic and Electrical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Mustafa B. A. Djamgoz
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Teuta Pilizota
- Systems and Synthetic Biology Centre and School of Biological Sciences, University of Edinburgh, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK
| | - Patrick R. Unwin
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Orkun S. Soyer
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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15
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Benarroch JM, Asally M. The Microbiologist’s Guide to Membrane Potential Dynamics. Trends Microbiol 2020; 28:304-314. [DOI: 10.1016/j.tim.2019.12.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
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16
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La Edwards C, Malyshev D, Stratford JP, Asally M. Rapid Detection of Proliferative Bacteria by Electrical Stimulation. Bio Protoc 2020; 10:e3508. [PMID: 33654734 DOI: 10.21769/bioprotoc.3508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/26/2019] [Accepted: 12/26/2019] [Indexed: 11/02/2022] Open
Abstract
Detecting live bacteria is an important task for antimicrobial susceptibility testing (AST) in the medical sector and for quality-monitoring in biological industries. Current methods for live-bacteria detection suffer limitations in speed or sensitivity. In a recent paper, we reported that electrical response dynamics in membrane potential enable single-cell rapid detection of live bacteria. The electrical response can be observed within a minute after electrical stimulation. Thus, it has potential in accelerating AST and the monitoring of biological samples. This method also enables experiments for biophysical and microbiological investigations into bacterial electrophysiology. With the hope that more researchers, scientists and engineers will use electrical stimulation for their assays, here we detail each step of the electrical stimulation experiment.
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Affiliation(s)
- Conor La Edwards
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, The United Kingdom
| | - Dmitry Malyshev
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, The United Kingdom
| | - James P Stratford
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, The United Kingdom
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, The United Kingdom
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17
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Sirec T, Benarroch JM, Buffard P, Garcia-Ojalvo J, Asally M. Electrical Polarization Enables Integrative Quality Control during Bacterial Differentiation into Spores. iScience 2019; 16:378-389. [PMID: 31226599 PMCID: PMC6586994 DOI: 10.1016/j.isci.2019.05.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/18/2018] [Accepted: 05/30/2019] [Indexed: 12/03/2022] Open
Abstract
Quality control of offspring is important for the survival of cells. However, the mechanisms by which quality of offspring cells may be checked while running genetic programs of cellular differentiation remain unclear. Here we investigated quality control during sporulating in Bacillus subtilis by combining single-cell time-lapse microscopy, molecular biology, and mathematical modeling. Our results revealed that the quality control via premature germination is coupled with the electrical polarization of outer membranes of developing forespores. The forespores that accumulate fewer cations on their surface are more likely to be aborted. This charge accumulation enables the projection of multi-dimensional information about the external environment and morphological development of the forespore into one-dimensional information of cation accumulation. We thus present a paradigm of cellular regulation by bacterial electrical signaling. Moreover, based on the insight we gain, we propose an electrophysiology-based approach of reducing the yield and quality of Bacillus endospores. Quality control during bacterial sporulation is coupled with cation accumulation Cation accumulation prevents premature germination Cation accumulation integrates information on morphological defects and environments Spores are less fit when sporulated with Thioflavin T
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Affiliation(s)
- Teja Sirec
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Jonatan M Benarroch
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK; Warwick Medical School, The University of Warwick, Coventry CV4 7AL, UK
| | - Pauline Buffard
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Munehiro Asally
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK; Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, UK; Bio-electrical Engineering Innovation Hub, The University of Warwick, Coventry CV4 7AL, UK.
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18
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Stratford JP, Edwards CLA, Ghanshyam MJ, Malyshev D, Delise MA, Hayashi Y, Asally M. Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity. Proc Natl Acad Sci U S A 2019; 116:9552-9557. [PMID: 31000597 PMCID: PMC6511025 DOI: 10.1073/pnas.1901788116] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Membrane-potential dynamics mediate bacterial electrical signaling at both intra- and intercellular levels. Membrane potential is also central to cellular proliferation. It is unclear whether the cellular response to external electrical stimuli is influenced by the cellular proliferative capacity. A new strategy enabling electrical stimulation of bacteria with simultaneous monitoring of single-cell membrane-potential dynamics would allow bridging this knowledge gap and further extend electrophysiological studies into the field of microbiology. Here we report that an identical electrical stimulus can cause opposite polarization dynamics depending on cellular proliferation capacity. This was demonstrated using two model organisms, namely Bacillus subtilis and Escherichia coli, and by developing an apparatus enabling exogenous electrical stimulation and single-cell time-lapse microscopy. Using this bespoke apparatus, we show that a 2.5-second electrical stimulation causes hyperpolarization in unperturbed cells. Measurements of intracellular K+ and the deletion of the K+ channel suggested that the hyperpolarization response is caused by the K+ efflux through the channel. When cells are preexposed to 400 ± 8 nm wavelength light, the same electrical stimulation depolarizes cells instead of causing hyperpolarization. A mathematical model extended from the FitzHugh-Nagumo neuron model suggested that the opposite response dynamics are due to the shift in resting membrane potential. As predicted by the model, electrical stimulation only induced depolarization when cells are treated with antibiotics, protonophore, or alcohol. Therefore, electrically induced membrane-potential dynamics offer a reliable approach for rapid detection of proliferative bacteria and determination of their sensitivity to antimicrobial agents at the single-cell level.
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Affiliation(s)
- James P Stratford
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, West Midlands, CV4 7AL,United Kingdom
| | - Conor L A Edwards
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Manjari J Ghanshyam
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Dmitry Malyshev
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Marco A Delise
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Yoshikatsu Hayashi
- Department of Biomedical Engineering, School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AH, United Kingdom
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom;
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, West Midlands, CV4 7AL,United Kingdom
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
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19
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Abstract
Metabolism is generally considered as a neatly organised system of modular pathways, shaped by evolution under selection for optimal cellular growth. This view falls short of explaining and predicting a number of key observations about the structure and dynamics of metabolism. We highlight these limitations of a pathway-centric view on metabolism and summarise studies suggesting how these could be overcome by viewing metabolism as a thermodynamically and kinetically constrained, dynamical flow system. Such a systems-level, first-principles based view of metabolism can open up new avenues of metabolic engineering and cures for metabolic diseases and allow better insights to a myriad of physiological processes that are ultimately linked to metabolism. Towards further developing this view, we call for a closer interaction among physical and biological disciplines and an increased use of electrochemical and biophysical approaches to interrogate cellular metabolism together with the microenvironment in which it exists.
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Affiliation(s)
- Christian Zerfaß
- Bio-Electrical Engineering (BEE) Innovation Hub, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Munehiro Asally
- Bio-Electrical Engineering (BEE) Innovation Hub, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, CV4 7AL, UK
| | - Orkun S. Soyer
- Bio-Electrical Engineering (BEE) Innovation Hub, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, CV4 7AL, UK
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20
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Jiang X, Zerfaß C, Feng S, Eichmann R, Asally M, Schäfer P, Soyer OS. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME J 2018; 12:1443-1456. [PMID: 29572468 PMCID: PMC5955953 DOI: 10.1038/s41396-018-0095-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/21/2023]
Abstract
A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environments requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a defined system to study the metabolic interactions in a spatial context among the plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis. Focusing on the growth dynamics of S. indica under defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found that S. indica growth is restored in thiamine-free media, when co-cultured with B. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact of B. subtilis was only visible when its inoculation was separated from that of S. indica either in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant seed treatments and for vertical farming under defined conditions.
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Affiliation(s)
- Xue Jiang
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Christian Zerfaß
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Song Feng
- Los Alamos National Laboratory, Theoretical Division (T-6), Center for Nonlinear Studies, Los Alamos, NM, 87545, USA
| | - Ruth Eichmann
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Munehiro Asally
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK.
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK.
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21
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Oka M, Moriyama T, Asally M, Kawakami K, Yoneda Y. Differential role for transcription factor Oct4 nucleocytoplasmic dynamics in somatic cell reprogramming and self-renewal of embryonic stem cells. J Biol Chem 2013; 288:15085-97. [PMID: 23580657 DOI: 10.1074/jbc.m112.448837] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oct4 is a member of the POU family of transcription factors and plays a critical role in both maintenance of the undifferentiated state of embryonic stem (ES) cells and in the reprogramming of somatic cells to induced pluripotent stem cells. Oct4 is imported into the nucleus where it functions as a transcription factor; however, the spatiotemporal dynamic behavior of Oct4 remains largely unknown. In the present study we show that Oct4 is a nucleocytoplasmic shuttling protein. Furthermore, although Oct4 mutants with altered nuclear import/export activity were able to maintain the self-renewal of ES cells, they displayed limited potential for cellular reprogramming. These results indicate that the intracellular localization of Oct4, which is dependent on nucleocytoplasmic shuttling, must be more strictly regulated for cellular reprogramming, suggesting that Oct4 plays differential roles in the self-renewal of ES cells and in somatic cell reprogramming.
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Affiliation(s)
- Masahiro Oka
- Biomolecular Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka, 565-0871 Japan
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22
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Asally M, Yasuda Y, Oka M, Otsuka S, Yoshimura SH, Takeyasu K, Yoneda Y. Nup358, a nucleoporin, functions as a key determinant of the nuclear pore complex structure remodeling during skeletal myogenesis. FEBS J 2011; 278:610-21. [PMID: 21205196 DOI: 10.1111/j.1742-4658.2010.07982.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nuclear pore complex (NPC) is the only gateway for molecular trafficking across the nuclear envelope. The NPC is not merely a static nuclear-cytoplasmic transport gate; the functional analysis of nucleoporins has revealed dynamic features of the NPC in various cellular functions, such as mitotic spindle formation and protein modification. However, it is not known whether the NPC undergoes dynamic changes during biological processes such as cell differentiation. In the present study, we evaluate changes in the expression levels of several nucleoporins and show that the amount of Nup358/RanBP2 within individual NPCs increases during muscle differentiation in C2C12 cells. Using atomic force microscopy, we demonstrate structural differences between the cytoplasmic surfaces of myoblast and myotube NPCs and a correlation between the copy number of Nup358 and the NPC structure. Furthermore, small interfering RNA-mediated depletion of Nup358 in myoblasts suppresses myotube formation without affecting cell viability, suggesting that NUP358 plays a role in myogenesis. These findings indicate that the NPC undergoes dynamic remodeling during muscle cell differentiation and that Nup358 is prominently involved in the remodeling process.
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Affiliation(s)
- Munehiro Asally
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, Japan
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23
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Oka M, Asally M, Yasuda Y, Ogawa Y, Tachibana T, Yoneda Y. The mobile FG nucleoporin Nup98 is a cofactor for Crm1-dependent protein export. Mol Biol Cell 2010; 21:1885-96. [PMID: 20375145 PMCID: PMC2877646 DOI: 10.1091/mbc.e09-12-1041] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/26/2010] [Accepted: 03/29/2010] [Indexed: 12/18/2022] Open
Abstract
Nup98 is a mobile nucleoporin that forms distinct dots in the nucleus, and, although a role for Nup98 in nuclear transport has been suggested, its precise function remains unclear. Here, we show that Nup98 plays an important role in Crm1-mediated nuclear protein export. Nuclear, but not cytoplasmic, dots of EGFP-tagged Nup98 disappeared rapidly after cell treatment with leptomycin B, a specific inhibitor of the nuclear export receptor, Crm1. Mutational analysis demonstrated that Nup98 physically and functionally interacts with Crm1 in a RanGTP-dependent manner through its N-terminal phenylalanine-glycine (FG) repeat region. Moreover, the activity of the Nup98-Crm1 complex was modulated by RanBP3, a known cofactor for Crm1-mediated nuclear export. Finally, cytoplasmic microinjection of anti-Nup98 inhibited the Crm1-dependent nuclear export of proteins, concomitant with the accumulation of anti-Nup98 in the nucleus. These results clearly demonstrate that Nup98 functions as a novel shuttling cofactor for Crm1-mediated nuclear export in conjunction with RanBP3.
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Affiliation(s)
- Masahiro Oka
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
- Department of Biochemistry, Graduate School of Medicine, Osaka University, and
- Japan Science and Technology Corporation (JST), Core Research for Evolution Science and Technology (CREST), Osaka University, Suita, Osaka 565-0871, Japan; and
| | - Munehiro Asally
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
| | - Yoshinari Yasuda
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
| | - Yutaka Ogawa
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
| | - Taro Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka 558-8585, Japan
| | - Yoshihiro Yoneda
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
- Department of Biochemistry, Graduate School of Medicine, Osaka University, and
- Japan Science and Technology Corporation (JST), Core Research for Evolution Science and Technology (CREST), Osaka University, Suita, Osaka 565-0871, Japan; and
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24
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Abstract
Npap60 (Nup50) is a nucleoporin that binds directly to importin α. In humans, there are two Npap60 isoforms: the long (Npap60L) and short (Npap60S) forms. Our results demonstrate that Npap60S stabilizes the binding of importin α to classical NLS-cargo, whereas Npap60L promotes the release of NLS-cargo from importin α. Npap60 (Nup50) is a nucleoporin that binds directly to importin α. In humans, there are two Npap60 isoforms: the long (Npap60L) and short (Npap60S) forms. In this study, we provide both in vitro and in vivo evidence that Npap60L and Npap60S function differently in nuclear protein import. In vitro binding assays revealed that Npap60S stabilizes the binding of importin α to classical NLS-cargo, whereas Npap60L promotes the release of NLS-cargo from importin α. In vivo time-lapse experiments showed that when the Npap60 protein level is controlled, allowing CAS to efficiently promote the dissociation of the Npap60/importin α complex, Npap60S and Npap60L suppress and accelerate the nuclear import of NLS-cargo, respectively. These results demonstrate that Npap60L and Npap60S have opposing functions and suggest that Npap60L and Npap60S levels must be carefully controlled for efficient nuclear import of classical NLS-cargo in humans. This study provides novel evidence that nucleoporin expression levels regulate nuclear import efficiency.
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Affiliation(s)
- Yutaka Ogawa
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, and Department of Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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25
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Yasuhara N, Shibazaki N, Tanaka S, Nagai M, Kamikawa Y, Oe S, Asally M, Kamachi Y, Kondoh H, Yoneda Y. Triggering neural differentiation of ES cells by subtype switching of importin-alpha. Nat Cell Biol 2006; 9:72-9. [PMID: 17159997 DOI: 10.1038/ncb1521] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 10/19/2006] [Indexed: 02/06/2023]
Abstract
Nuclear proteins are selectively imported into the nucleus by transport factors such as importin-alpha and importin-beta. Here, we show that the expression of importin-alpha subtypes is strictly regulated during neural differentiation of mouse embryonic stem (ES) cells, and that the switching of importin-alpha subtype expression is critical for neural differentiation. Moreover, reproducing the switching of importin-alpha subtype expression in undifferentiated ES cells induced neural differentiation in the presence of leukaemia inhibitory factor (LIF) and serum, coordinated with the regulated expression of Oct3/4, Brn2 and SOX2, which are involved in ES-neural identity determination. These transcription factors were selectively imported into the nucleus by specific subtypes of importin-alpha. Thus, importin-alpha subtype switching has a major impact on cell differentiation through the regulated nuclear import of a specific set of transcription factors. This is the first study to propose that transport factors should be considered as major players in cell-fate determination.
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Affiliation(s)
- Noriko Yasuhara
- Department of Cell Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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26
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Asally M, Yoneda Y. β-Catenin can act as a nuclear import receptor for its partner transcription factor, lymphocyte enhancer factor-1 (lef-1). Exp Cell Res 2005; 308:357-63. [PMID: 15936755 DOI: 10.1016/j.yexcr.2005.05.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 04/28/2005] [Accepted: 05/10/2005] [Indexed: 01/11/2023]
Abstract
Nuclear accumulation of beta-catenin plays an important role in the Wnt signaling pathway. In the nucleus, beta-catenin acts as a transcriptional co-activator for TCF/LEF family of transcription factors. It has been shown that lef-1 contains a typical basic type nuclear localization signal (NLS) and is transported into the nucleus by the conventional import pathway. In this study, we found that a mutant lef-1 lacking the classical NLS accumulated in the nucleus of living cells, when beta-catenin was co-expressed. In addition, in a cell-free import assay, lef-1 migrated into the nucleus in the presence of beta-catenin alone without any other soluble factors. In contrast, another mutant lef-1 lacking the beta-catenin binding domain failed to migrate into the nucleus, even in the presence of beta-catenin. These findings indicate that beta-catenin alone can mediate the nuclear import of lef-1 through the direct binding. Collectively, we propose that there are two distinct pathways for the nuclear import of lef-1: importin alpha/beta-mediated and beta-catenin-mediated one, which provides a novel paradigm for Wnt signaling pathway.
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Affiliation(s)
- Munehiro Asally
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Graduate School of Medicine, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
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