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Yang Z, Pang Q, Zhou J, Xuan C, Xie S. Leveraging aptamers for targeted protein degradation. Trends Pharmacol Sci 2023; 44:776-785. [PMID: 37380531 DOI: 10.1016/j.tips.2023.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
Targeted protein degradation (TPD) technologies, particularly proteolysis-targeting chimeras (PROTACs), have emerged as a significant advancement in drug discovery. However, several hurdles - such as the difficulty of identifying suitable ligands for traditionally undruggable proteins, poor solubility and impermeability, nonspecific biodistribution, and on-target off-tissue toxicity - present challenges to their clinical applications. Aptamers are promising ligands for broad-ranging molecular recognition. Utilizing aptamers in TPD has shown potential advantages in overcoming these challenges. Here, we provide an overview of recent developments in aptamer-based TPD, emphasizing their potential to achieve targeted delivery and their promise for the spatiotemporal degradation of undruggable proteins. We also discuss the challenges and future directions of aptamer-based TPD with the goal of facilitating their clinical applications.
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Affiliation(s)
- Zhihao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China
| | - Qiuxiang Pang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China; Department of Genetics and Cell Biology, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenghao Xuan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China.
| | - Songbo Xie
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China; Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China.
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2
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Zheng Y, Hu W. Editorial: Spatiotemporal regulation of central nervous system disorders: molecular mechanisms and emerging techniques. Front Cell Dev Biol 2023; 11:1301013. [PMID: 37868910 PMCID: PMC10588469 DOI: 10.3389/fcell.2023.1301013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023] Open
Affiliation(s)
- Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, School of Basic Medical Sciences, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Weiwei Hu
- NHC and CAMS Key Laboratory of Medical Neurobiology, Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, School of Basic Medical Sciences, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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3
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Jian G, Li D, Ying Q, Chen X, Zhai Q, Wang S, Mei L, Cannon RD, Ji P, Liu W, Wang H, Chen T. Dual Photo-Enhanced Interpenetrating Network Hydrogel with Biophysical and Biochemical Signals for Infected Bone Defect Healing. Adv Healthc Mater 2023; 12:e2300469. [PMID: 37462929 DOI: 10.1002/adhm.202300469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/19/2023] [Indexed: 07/29/2023]
Abstract
The healing of infected bone defects (IBD) is a complex physiological process involving a series of spatially and temporally overlapping events, including pathogen clearance, immunological modulation, vascularization, and osteogenesis. Based on the theory that bone healing is regulated by both biochemical and biophysical signals, in this study, a copper doped bioglass (CuBGs)/methacryloyl-modified gelatin nanoparticle (MA-GNPs)/methacrylated silk fibroin (SilMA) hybrid hydrogel is developed to promote IBD healing. This hybrid hydrogel demonstrates a dual-photocrosslinked interpenetrating network mechanism, wherein the photocrosslinked SilMA as the main network ensures structural integrity, and the photocrosslinked MA-GNPs colloidal network increases strength and dissipates loading forces. In an IBD model, the hydrogel exhibits excellent biophysical characteristics, such as adhesion, adaptation to irregular defect shapes, and in situ physical reinforcement. At the same time, by sequentially releasing bioactive ions such as Cu2+ , Ca2+ , and Si2+ ions from CuBGs on demand, the hydrogel spatiotemporally coordinates antibacterial, immunomodulatory and bone remodeling events, efficiently removing infection and accelerating bone repair without the use of antibiotics or exogenous recombinant proteins. Therefore, the hybrid hydrogel can be used as a simple and effective method for the treatment of IBD.
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Affiliation(s)
- Guangyu Jian
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Dize Li
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Qiwei Ying
- Key State Laboratory of Fine Chemicals, School of Bioengineering, Dalian University of Technology, Dalian, 116023, P. R. China
| | - Xu Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Qiming Zhai
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Si Wang
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Li Mei
- Department of Oral Sciences, Sir John Walsh Research Institute Faculty of Dentistry, University of Otago, Dunedin, 9054, New Zealand
| | - Richard D Cannon
- Department of Oral Sciences, Sir John Walsh Research Institute Faculty of Dentistry, University of Otago, Dunedin, 9054, New Zealand
| | - Ping Ji
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Wenzhao Liu
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
| | - Huanan Wang
- Key State Laboratory of Fine Chemicals, School of Bioengineering, Dalian University of Technology, Dalian, 116023, P. R. China
| | - Tao Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, 401147, P. R. China
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4
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Ferber SG, Weller A, Soreq H. Control systems theory revisited: new insights on the brain clocks of time-to-action. Front Neurosci 2023; 17:1171765. [PMID: 37378011 PMCID: PMC10292755 DOI: 10.3389/fnins.2023.1171765] [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: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
To outline the complex biological rhythms underlying the time-to-action of goal-oriented behavior in the adult brain, we employed a Boolean Algebra model based on Control Systems Theory. This suggested that "timers" of the brain reflect a metabolic excitation-inhibition balance and that healthy clocks underlying goal-oriented behavior (optimal range of signal variability) are maintained by XOR logic gates in parallel sequences between cerebral levels. Using truth tables, we found that XOR logic gates reflect healthy, regulated time-to-action events between levels. We argue that the brain clocks of time-to-action are active within multileveled, parallel-sequence complexes shaped by experience. We show the metabolic components of time-to-action in levels ranging from the atom level through molecular, cellular, network and inter-regional levels, operating as parallel sequences. We employ a thermodynamic perspective, suggest that clock genes calculate free energy versus entropy and derived time-to-action level-wise as a master controller, and show that they are receivers, as well as transmitters of information. We argue that regulated multileveled time-to-action processes correspond to Boltzmann's thermodynamic theorem of micro- and macro-states, and that the available metabolic free-energy-entropy matrix determines the brain's reversible states for its age-appropriate chrono-properties at given moments. Thus, healthy timescales are not a precise number of nano- or milliseconds of activity nor a simple phenotypic distinction between slow vs. quick time-to-action, but rather encompass a range of variability, which depends on the molecules' size and dynamics with the composition of receptors, protein and RNA isoforms.
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Affiliation(s)
- Sari Goldstein Ferber
- Department of Psychology, Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- Department of Psychology and Brain Sciences, University of Delaware, Newark, DE, United States
| | - Aron Weller
- Department of Psychology, Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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5
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Jiang Y, Ding P. Calcium signaling in plant immunity: a spatiotemporally controlled symphony. Trends Plant Sci 2023; 28:74-89. [PMID: 36504136 DOI: 10.1016/j.tplants.2022.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Calcium ions (Ca2+) are prominent intracellular messengers in all eukaryotic cells. Recent studies have emphasized the crucial roles of Ca2+ in plant immunity. Here, we review the latest progress on the spatiotemporal control of Ca2+ function in plant immunity. We discuss discoveries of how Ca2+ influx is triggered upon the activation of immune receptors, how Ca2+-permeable channels are activated, how Ca2+ signals are decoded inside plant cells, and how these signals are switched off. Despite recent advances, many open questions remain and we highlight the existing toolkit and the new technologies to address the outstanding questions of Ca2+ signaling in plant immunity.
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Affiliation(s)
- Yuxiang Jiang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Pingtao Ding
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333, BE, The Netherlands.
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6
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Takada S, Yoshinaga N, Doi N, Fujiwara K. Controlling the Periodicity of a Reaction-Diffusion Wave in Artificial Cells by a Two-Way Energy Supplier. ACS Nano 2022; 16:16853-16861. [PMID: 36214379 DOI: 10.1021/acsnano.2c06756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Reaction-diffusion (RD) waves, which are dynamic self-organization structures generated by nanosize molecules, are a fundamental mechanism from patterning in nano- and micromaterials to spatiotemporal regulations in living cells, such as cell division and motility. Although the periods of RD waves are the critical element for these functions, the development of a system to control their period is challenging because RD waves result from nonlinear physical dynamics under far-from-equilibrium conditions. Here, we developed an artificial cell system with tunable period of an RD-driven wave (Min protein wave), which determines a cell division site plane in living bacterial cells. The developed system is based on our finding that Min waves are generated by energy consumption of either ATP or dATP, and the period of the wave is different between these two energy suppliers. We showed that the Min-wave period was modulated linearly by the mixing ratio of ATP and dATP and that it was also possible to estimate the mixing ratio of ATP and dATP from the period. Our findings illuminated a previously unidentified principle to control the dissipative dynamics of biomolecules and, simultaneously, built an important framework to construct molecular robots with spatiotemporal units.
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Affiliation(s)
- Sakura Takada
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, AIST, Sendai 980-8577, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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7
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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8
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Zhou X, Mehta S, Zhang J. Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks. Trends Biochem Sci 2020; 45:889-905. [PMID: 32660810 PMCID: PMC7502535 DOI: 10.1016/j.tibs.2020.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 01/11/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Cell signaling networks are intricately regulated in time and space to determine the responses and fates of cells to different cues. Genetically encodable fluorescent and bioluminescent biosensors enable the direct visualization of these spatiotemporal signaling dynamics within the native biological context, and have therefore become powerful molecular tools whose unique benefits are being used to address challenging biological questions. We first review the basis of biosensor design and remark on recent technologies that are accelerating biosensor development. We then discuss a few of the latest advances in the development and application of genetically encodable fluorescent and bioluminescent biosensors that have led to scientific or technological breakthroughs.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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9
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Nothling MD, Fu Q, Reyhani A, Allison‐Logan S, Jung K, Zhu J, Kamigaito M, Boyer C, Qiao GG. Progress and Perspectives Beyond Traditional RAFT Polymerization. Adv Sci (Weinh) 2020; 7:2001656. [PMID: 33101866 PMCID: PMC7578854 DOI: 10.1002/advs.202001656] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/17/2020] [Indexed: 05/09/2023]
Abstract
The development of advanced materials based on well-defined polymeric architectures is proving to be a highly prosperous research direction across both industry and academia. Controlled radical polymerization techniques are receiving unprecedented attention, with reversible-deactivation chain growth procedures now routinely leveraged to prepare exquisitely precise polymer products. Reversible addition-fragmentation chain transfer (RAFT) polymerization is a powerful protocol within this domain, where the unique chemistry of thiocarbonylthio (TCT) compounds can be harnessed to control radical chain growth of vinyl polymers. With the intense recent focus on RAFT, new strategies for initiation and external control have emerged that are paving the way for preparing well-defined polymers for demanding applications. In this work, the cutting-edge innovations in RAFT that are opening up this technique to a broader suite of materials researchers are explored. Emerging strategies for activating TCTs are surveyed, which are providing access into traditionally challenging environments for reversible-deactivation radical polymerization. The latest advances and future perspectives in applying RAFT-derived polymers are also shared, with the goal to convey the rich potential of RAFT for an ever-expanding range of high-performance applications.
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Affiliation(s)
- Mitchell D. Nothling
- Polymer Science GroupDepartment of Chemical EngineeringThe University of MelbourneParkvilleVIC3010Australia
| | - Qiang Fu
- Centre for Technology in Water and Wastewater Treatment (CTWW)School of Civil and Environmental EngineeringUniversity of Technology SydneyUltimoNSW2007Australia
| | - Amin Reyhani
- Polymer Science GroupDepartment of Chemical EngineeringThe University of MelbourneParkvilleVIC3010Australia
| | - Stephanie Allison‐Logan
- Polymer Science GroupDepartment of Chemical EngineeringThe University of MelbourneParkvilleVIC3010Australia
| | - Kenward Jung
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN)School of Chemical EngineeringUNWSSydneyNSW2052Australia
| | - Jian Zhu
- College of ChemistryChemical Engineering and Material ScienceDepartment of Polymer Science and EngineeringSoochow UniversitySuzhou215123China
| | - Masami Kamigaito
- Department of Molecular and Macromolecular ChemistryGraduate School of EngineeringNagoya UniversityFuro‐cho, Chikusa‐kuNagoya464‐8603Japan
| | - Cyrille Boyer
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN)School of Chemical EngineeringUNWSSydneyNSW2052Australia
| | - Greg G. Qiao
- Polymer Science GroupDepartment of Chemical EngineeringThe University of MelbourneParkvilleVIC3010Australia
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10
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Li Y, Wang L, Yuan L, Song Y, Sun J, Jia Q, Xie Q, Xu X. Molecular investigation of organ-autonomous expression of Arabidopsis circadian oscillators. Plant Cell Environ 2020; 43:1501-1512. [PMID: 32012302 DOI: 10.1111/pce.13739] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
The circadian pacemaker in plants is a hierarchical multioscillator system that directs and maintains a 24-hr oscillation required for organism homeostasis and environmental fitness. Molecular clockwork within individual tissues and organs acts cell autonomously, showing differences in circadian expression of core oscillators and their target genes; there are functional dominance and coupling in the complex regulatory network. However, molecular characteristics of organ-specific clocks are still unknown. Here, we showed the detached shoot and root possess dynamic circadian protein-protein interactions between clock core components, periodicity in organs exhibits a difference. The period length difference between shoot and root was not remarkable in prr7-3 and prr7-3 prr9-1 mutants. In addition, the phase transition curve indicated that shoot and root clock respond differently to the resetting cues of ambient temperature. PRR9 and PRR7 compensate circadian period between 22°C and 28°C in shoot, not in root. The circadian rhythms of PRR9 or PRR7 transcript accumulation showed no difference at 22°C and 28°C in shoot, but differences were observed in root. In summary, our results reveal the specificity of dynamic circadian protein-protein interactions in organ-autonomous clocks and the critical roles of PRR9 and PRR7 in mechanisms regulating temperature compensation in aerial shoot system.
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Affiliation(s)
- Yue Li
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lingbao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Yuan
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yang Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Junqiu Sun
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qian Jia
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Qiguang Xie
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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11
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Kohyama S, Yoshinaga N, Yanagisawa M, Fujiwara K, Doi N. Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells. eLife 2019; 8:44591. [PMID: 31358115 PMCID: PMC6667215 DOI: 10.7554/elife.44591] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 12/21/2018] [Accepted: 07/12/2019] [Indexed: 01/10/2023] Open
Abstract
The Min system, a system that determines the bacterial cell division plane, uses changes in the localization of proteins (a Min wave) that emerges by reaction-diffusion coupling. Although previous studies have shown that space sizes and boundaries modulate the shape and speed of Min waves, their effects on wave emergence were still elusive. Here, by using a microsized fully confined space to mimic live cells, we revealed that confinement changes the conditions for the emergence of Min waves. In the microsized space, an increased surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary for the stable generation of Min waves. Furthermore, we showed that the cell-sized space strictly limits parameters for wave emergence because confinement inhibits both the instability and excitability of the system. These results show that confinement of reaction-diffusion systems has the potential to control spatiotemporal patterns in live cells.
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Affiliation(s)
- Shunshi Kohyama
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University Katahira, Sendai, Japan.,MathAM-OIL, AIST, Sendai, Japan
| | - Miho Yanagisawa
- Department of Basic Science, Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
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12
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Gupta DB, Rai Y, Gayali S, Chakraborty S, Chakraborty N. Plant Organellar Proteomics in Response to Dehydration: Turning Protein Repertoire into Insights. Front Plant Sci 2016; 7:460. [PMID: 27148291 PMCID: PMC4829595 DOI: 10.3389/fpls.2016.00460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/24/2016] [Indexed: 05/29/2023]
Abstract
Stress adaptation or tolerance in plants is a complex phenomenon involving changes in physiological and metabolic processes. Plants must develop elaborate networks of defense mechanisms, and adapt to and survive for sustainable agriculture. Water-deficit or dehydration is the most critical environmental factor that plants are exposed to during their life cycle, which influences geographical distribution and productivity of many crop species. The cellular responses to dehydration are orchestrated by a series of multidirectional relays of biochemical events at organelle level. The new challenge is to dissect the underlying mechanisms controlling the perception of stress signals and their transmission to cellular machinery for activation of adaptive responses. The completeness of current descriptions of spatial distribution of proteins, the relevance of subcellular locations in diverse functional processes, and the changes of protein abundance in response to dehydration hold the key to understanding how plants cope with such stress conditions. During past decades, organellar proteomics has proved to be useful not only for deciphering reprograming of plant responses to dehydration, but also to dissect stress-responsive pathways. This review summarizes a range of organellar proteomics investigations under dehydration to gain a holistic view of plant responses to water-deficit conditions, which may facilitate future efforts to develop genetically engineered crops for better adaptation.
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Affiliation(s)
- Deepti B. Gupta
- Department of Biotechnology, TERI UniversityNew Delhi, India
| | - Yogita Rai
- Department of Biotechnology, TERI UniversityNew Delhi, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
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