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Žárský V, Nielsen ME, Blatt MR. Formins, cell wall integrity, ROP guanine exchange factors, secretion regulators, and small secreted peptides in plant cell exocytosis and defence. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3665-3667. [PMID: 38910337 DOI: 10.1093/jxb/erae230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Affiliation(s)
- Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic
| | - Mads Eggert Nielsen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center (CPSC), University of Copenhagen, Denmark
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK
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2
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Shao X, Zhang Z, Yang F, Yu Y, Guo J, Li J, Xu T, Pan X. Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1390993. [PMID: 38872895 PMCID: PMC11170286 DOI: 10.3389/fpls.2024.1390993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024]
Abstract
Tobacco (Nicotiana tabacum L.) is an important industrial crop, which is sensitive to chilling stress. Tobacco seedlings that have been subjected to chilling stress readily flower early, which seriously affects the yield and quality of their leaves. Currently, there has been progress in elucidating the molecular mechanisms by which tobacco responds to chilling stress. However, little is known about the phosphorylation that is mediated by chilling. In this study, the transcriptome, proteome and phosphoproteome were analyzed to elucidate the mechanisms of the responses of tobacco shoot and root to chilling stress (4 °C for 24 h). A total of 6,113 differentially expressed genes (DEGs), 153 differentially expressed proteins (DEPs) and 345 differential phosphopeptides were identified in the shoot, and the corresponding numbers in the root were 6,394, 212 and 404, respectively. This study showed that the tobacco seedlings to 24 h of chilling stress primarily responded to this phenomenon by altering their levels of phosphopeptide abundance. Kyoto Encyclopedia of Genes and Genomes analyses revealed that starch and sucrose metabolism and endocytosis were the common pathways in the shoot and root at these levels. In addition, the differential phosphopeptide corresponding proteins were also significantly enriched in the pathways of photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms in the shoot and arginine and proline metabolism, peroxisome and RNA transport in the root. These results suggest that phosphoproteins in these pathways play important roles in the response to chilling stress. Moreover, kinases and transcription factors (TFs) that respond to chilling at the levels of phosphorylation are also crucial for resistance to chilling in tobacco seedlings. The phosphorylation or dephosphorylation of kinases, such as CDPKs and RLKs; and TFs, including VIP1-like, ABI5-like protein 2, TCP7-like, WRKY 6-like, MYC2-like and CAMTA7 among others, may play essential roles in the transduction of tobacco chilling signal and the transcriptional regulation of the genes that respond to chilling stress. Taken together, these findings provide new insights into the molecular mechanisms and regulatory networks of the responses of tobacco to chilling stress.
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Affiliation(s)
- Xiuhong Shao
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Zhenchen Zhang
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Faheng Yang
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Yongchao Yu
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Junjie Guo
- China National Tobacco Corporation, Guangdong Company, Guangzhou, China
| | - Jiqin Li
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Tingyu Xu
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
| | - Xiaoying Pan
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangzhou, China
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Modic M, Adamek M, Ule J. The impact of IDR phosphorylation on the RNA binding profiles of proteins. Trends Genet 2024:S0168-9525(24)00078-7. [PMID: 38705823 DOI: 10.1016/j.tig.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Due to their capacity to mediate repetitive protein interactions, intrinsically disordered regions (IDRs) are crucial for the formation of various types of protein-RNA complexes. The functions of IDRs are strongly modulated by post-translational modifications (PTMs). Phosphorylation is the most common and well-studied modification of IDRs, which can alter homomeric or heteromeric interactions of proteins and impact their ability to phase separate. Moreover, phosphorylation can influence the RNA-binding properties of proteins, and recent studies demonstrated its selective impact on the global profiles of protein-RNA binding and regulation. These findings highlight the need for further integrative approaches to understand how signalling remodels protein-RNA networks in cells.
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Affiliation(s)
- Miha Modic
- National Institute of Chemistry, Ljubljana, Slovenia; The Francis Crick Institute, London, UK; UK Dementia Research Institute at King's College London, London, UK.
| | - Maksimiljan Adamek
- National Institute of Chemistry, Ljubljana, Slovenia; PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Ljubljana, Slovenia; The Francis Crick Institute, London, UK; UK Dementia Research Institute at King's College London, London, UK.
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4
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Ren Y, Yang J, Fujita B, Jin H, Zhang Y, Berro J. Force redistribution in clathrin-mediated endocytosis revealed by coiled-coil force sensors. SCIENCE ADVANCES 2023; 9:eadi1535. [PMID: 37831774 PMCID: PMC10575576 DOI: 10.1126/sciadv.adi1535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Forces are central to countless cellular processes, yet in vivo force measurement at the molecular scale remains difficult if not impossible. During clathrin-mediated endocytosis, forces produced by the actin cytoskeleton are transmitted to the plasma membrane by a multiprotein coat for membrane deformation. However, the magnitudes of these forces remain unknown. Here, we present new in vivo force sensors that induce protein condensation under force. We measured the forces on the fission yeast Huntingtin-Interacting Protein 1 Related (HIP1R) homolog End4p, a protein that links the membrane to the actin cytoskeleton. End4p is under ~19-piconewton force near the actin cytoskeleton, ~11 piconewtons near the clathrin lattice, and ~9 piconewtons near the plasma membrane. Our results demonstrate that forces are collected and redistributed across the endocytic machinery.
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Affiliation(s)
- Yuan Ren
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Jie Yang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Barbara Fujita
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Huaizhou Jin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yongli Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
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5
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Miao Y, Guo X, Zhu K, Zhao W. Biomolecular condensates tunes immune signaling at the Host-Pathogen interface. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102374. [PMID: 37148673 DOI: 10.1016/j.pbi.2023.102374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
Membraneless organelles participate in diverse spatiotemporal regulation of cellular signal transduction by recruiting necessary signaling factors. During host-pathogen interactions, the plasma membrane (PM) at the interface between the plant and microbes serves as a central platform for forming multicomponent immune signaling hubs. The macromolecular condensation of the immune complex and regulators is important in regulating immune signaling outputs regarding strength, timing, and crosstalk between signaling pathways. This review discusses mechanisms that regulate specific and crosstalk of plant immune signal transduction pathways through macromolecular assembly and condensation.
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Affiliation(s)
- Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore.
| | - Xiangfu Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore
| | - Kexin Zhu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, 637457, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore
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6
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Li R, Pang L. Comparing the effects of proteins with IDRs on membrane system in yeast, mammalian cells, and the model plant Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102375. [PMID: 37172364 DOI: 10.1016/j.pbi.2023.102375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/26/2023] [Accepted: 04/07/2023] [Indexed: 05/14/2023]
Abstract
Membrane vesiculation is an energy-costing process. Previous studies paid much attention to proteins with curvature-inducing motifs. Recent publications reveal that the liquid-like protein assembly on membrane surfaces provides an efficient yet structure-independent mechanism for increasing the membrane curvature, which plays important roles in vesicle transport in many aspects. Intrinsically disordered regions (IDRs) within the proteins are highly potent drivers of membrane curvature by providing large hydrodynamic radii to generate steric pressure. Biomolecular condensates formed by phase separation can provide a reaction platform for sequential processes or generate a wetting surface to sequestrate cargos and trigger membrane remodeling. We review the latest progress in yeast and mammalian cells, focus on the mechanism of clathrin-mediated endocytosis (CME) and autophagy initiation, and compare with what we know in model plant Arabidopsis. The comparison may give important insights into the understanding of basic membrane trafficking mechanisms in plant cells.
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Affiliation(s)
- Ruixi Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Lei Pang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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Han X, Hu Z, Surya W, Ma Q, Zhou F, Nordenskiöld L, Torres J, Lu L, Miao Y. The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization. Cell Rep 2023; 42:112594. [PMID: 37269287 DOI: 10.1016/j.celrep.2023.112594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/21/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Coronins play critical roles in actin network formation. The diverse functions of coronins are regulated by the structured N-terminal β propeller and the C-terminal coiled coil (CC). However, less is known about a middle "unique region" (UR), which is an intrinsically disordered region (IDR). The UR/IDR is an evolutionarily conserved signature in the coronin family. By integrating biochemical and cell biology experiments, coarse-grained simulations, and protein engineering, we find that the IDR optimizes the biochemical activities of coronins in vivo and in vitro. The budding yeast coronin IDR plays essential roles in regulating Crn1 activity by fine-tuning CC oligomerization and maintaining Crn1 as a tetramer. The IDR-guided optimization of Crn1 oligomerization is critical for F-actin cross-linking and regulation of Arp2/3-mediated actin polymerization. The final oligomerization status and homogeneity of Crn1 are contributed by three examined factors: helix packing, the energy landscape of the CC, and the length and molecular grammar of the IDR.
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Affiliation(s)
- Xiao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zixin Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Feng Zhou
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore 636921, Singapore.
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8
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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9
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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10
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Ma Z, Zhu K, Gao Y, Tan S, Miao Y. Molecular condensation and mechanoregulation of plant class I formin, an integrin‐like actin nucleator. FEBS J 2022. [DOI: 10.1111/febs.16571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/29/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Zhiming Ma
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
| | - Kexin Zhu
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
| | - Yong‐Gui Gao
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
| | - Suet‐Mien Tan
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
| | - Yansong Miao
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- Institute for Digital Molecular Analytics and Science Nanyang Technological University Singapore City Singapore
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11
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Wood TE, Westervelt KA, Yoon JM, Eshleman HD, Levy R, Burnes H, Slade DJ, Lesser CF, Goldberg MB. The Shigella Spp. Type III Effector Protein OspB Is a Cysteine Protease. mBio 2022; 13:e0127022. [PMID: 35638611 PMCID: PMC9239218 DOI: 10.1128/mbio.01270-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
The type III secretion system is required for virulence of many pathogenic bacteria. Bacterial effector proteins delivered into target host cells by this system modulate host signaling pathways and processes in a manner that promotes infection. Here, we define the activity of the effector protein OspB of the human pathogen Shigella spp., the etiological agent of shigellosis and bacillary dysentery. Using the yeast Saccharomyces cerevisiae as a model organism, we show that OspB sensitizes cells to inhibition of TORC1, the central regulator of growth and metabolism. In silico analyses reveal that OspB bears structural homology to bacterial cysteine proteases that target mammalian cell processes, and we define a conserved cysteine-histidine catalytic dyad required for OspB function. Using yeast genetic screens, we identify a crucial role for the arginine N-degron pathway in the yeast growth inhibition phenotype and show that inositol hexakisphosphate is an OspB cofactor. We find that a yeast substrate for OspB is the TORC1 component Tco89p, proteolytic cleavage of which generates a C-terminal fragment that is targeted for degradation via the arginine N-degron pathway; processing and degradation of Tco89p is required for the OspB phenotype. In all, we demonstrate that the Shigella T3SS effector OspB is a cysteine protease and decipher its interplay with eukaryotic cell processes. IMPORTANCEShigella spp. are important human pathogens and among the leading causes of diarrheal mortality worldwide, especially in children. Virulence depends on the Shigella type III secretion system (T3SS). Definition of the roles of the bacterial effector proteins secreted by the T3SS is key to understanding Shigella pathogenesis. The effector protein OspB contributes to a range of phenotypes during infection, yet the mechanism of action is unknown. Here, we show that S. flexneri OspB possesses cysteine protease activity in both yeast and mammalian cells, and that enzymatic activity of OspB depends on a conserved cysteine-histidine catalytic dyad. We determine how its protease activity sensitizes cells to TORC1 inhibition in yeast, finding that OspB cleaves a component of yeast TORC1, and that the degradation of the C-terminal cleavage product is responsible for OspB-mediated hypersensitivity to TORC1 inhibitors. Thus, OspB is a cysteine protease that depends on a conserved cysteine-histidine catalytic dyad.
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Affiliation(s)
- Thomas E. Wood
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathleen A. Westervelt
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jessica M. Yoon
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Heather D. Eshleman
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Roie Levy
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Henry Burnes
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel J. Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Cammie F. Lesser
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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12
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Adnane S, Marino A, Leucci E. LncRNAs in human cancers: signal from noise. Trends Cell Biol 2022; 32:565-573. [DOI: 10.1016/j.tcb.2022.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 12/31/2022]
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13
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Ma Z, Sun Y, Zhu X, Yang L, Chen X, Miao Y. Membrane nanodomains modulate formin condensation for actin remodeling in Arabidopsis innate immune responses. THE PLANT CELL 2022; 34:374-394. [PMID: 34726756 PMCID: PMC8774048 DOI: 10.1093/plcell/koab261] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/20/2021] [Indexed: 05/23/2023]
Abstract
The assembly of macromolecules on the plasma membrane concentrates cell surface biomolecules into nanometer- to micrometer-scale clusters (nano- or microdomains) that help the cell initiate or respond to signals. In plant-microbe interactions, the actin cytoskeleton undergoes rapid remodeling during pathogen-associated molecular pattern-triggered immunity (PTI). The nanoclustering of formin-actin nucleator proteins at the cell surface has been identified as underlying actin nucleation during plant innate immune responses. Here, we show that the condensation of nanodomain constituents and the self-assembly of remorin proteins enables this mechanism of controlling formin condensation and activity during innate immunity in Arabidopsis thaliana. Through intrinsically disordered region-mediated remorin oligomerization and formin interaction, remorin gradually recruits and condenses formins upon PTI activation in lipid bilayers, consequently increasing actin nucleation in a time-dependent manner postinfection. Such nanodomain- and remorin-mediated regulation of plant surface biomolecules is expected to be a general feature of plant innate immune responses that creates spatially separated biochemical compartments and fine tunes membrane physicochemical properties for transduction of immune signals in the host.
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Affiliation(s)
- Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yanbiao Sun
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Centre, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinlu Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Centre, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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14
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Xie Y, Zhou F, Ma Q, Lu L, Miao Y. A teamwork promotion of formin-mediated actin nucleation by Bud6 and Aip5 in Saccharomyces cerevisiae. Mol Biol Cell 2021; 33:ar19. [PMID: 34818061 PMCID: PMC9236144 DOI: 10.1091/mbc.e21-06-0285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actin nucleation is achieved by collaborative teamwork of actin nucleator factors (NFs) and nucleation-promoting factors (NPFs) into functional protein complexes. Selective inter- and intramolecular interactions between the nucleation complex constituents enable diverse modes of complex assembly in initiating actin polymerization on demand. Budding yeast has two formins, Bni1 and Bnr1, which are teamed up with different NPFs. However, the selective pairing between formin NFs and NPFs into the nucleation core for actin polymerization is not completely understood. By examining the functions and interactions of NPFs and NFs via biochemistry, genetics, and mathematical modeling approaches, we found that two NPFs, Aip5 and Bud6, showed joint teamwork effort with Bni1 and Bnr1, respectively, by interacting with the C-terminal intrinsically disordered region (IDR) of formin, in which two NPFs work together to promote formin-mediated actin nucleation. Although the C-terminal IDRs of Bni1 and Bnr1 are distinct in length, each formin IDR orchestrates the recruitment of Bud6 and Aip5 cooperatively by different positioning strategies to form a functional complex. Our study demonstrated the dynamic assembly of the actin nucleation complex by recruiting multiple partners in budding yeast, which may be a general feature for effective actin nucleation by formins.
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Affiliation(s)
- Ying Xie
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Feng Zhou
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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15
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Boyko KV, Rosenkranz EA, Smith DM, Miears HL, Oueld es cheikh M, Lund MZ, Young JC, Reardon PN, Okon M, Smirnov SL, Antos JM. Sortase-mediated segmental labeling: A method for segmental assignment of intrinsically disordered regions in proteins. PLoS One 2021; 16:e0258531. [PMID: 34710113 PMCID: PMC8553144 DOI: 10.1371/journal.pone.0258531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
A significant number of proteins possess sizable intrinsically disordered regions (IDRs). Due to the dynamic nature of IDRs, NMR spectroscopy is often the tool of choice for characterizing these segments. However, the application of NMR to IDRs is often hindered by their instability, spectral overlap and resonance assignment difficulties. Notably, these challenges increase considerably with the size of the IDR. In response to these issues, here we report the use of sortase-mediated ligation (SML) for segmental isotopic labeling of IDR-containing samples. Specifically, we have developed a ligation strategy involving a key segment of the large IDR and adjacent folded headpiece domain comprising the C-terminus of A. thaliana villin 4 (AtVLN4). This procedure significantly reduces the complexity of NMR spectra and enables group identification of signals arising from the labeled IDR fragment, a process we refer to as segmental assignment. The validity of our segmental assignment approach is corroborated by backbone residue-specific assignment of the IDR using a minimal set of standard heteronuclear NMR methods. Using segmental assignment, we further demonstrate that the IDR region adjacent to the headpiece exhibits nonuniform spectral alterations in response to temperature. Subsequent residue-specific characterization revealed two segments within the IDR that responded to temperature in markedly different ways. Overall, this study represents an important step toward the selective labeling and probing of target segments within much larger IDR contexts. Additionally, the approach described offers significant savings in NMR recording time, a valuable advantage for the study of unstable IDRs, their binding interfaces, and functional mechanisms.
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Affiliation(s)
- Kristina V. Boyko
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Erin A. Rosenkranz
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Derrick M. Smith
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Heather L. Miears
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Melissa Oueld es cheikh
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Micah Z. Lund
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Jeffery C. Young
- Department of Biology, Western Washington University, Bellingham, Washington, United States of America
| | - Patrick N. Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
- * E-mail: (JMA); (SLS)
| | - John M. Antos
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
- * E-mail: (JMA); (SLS)
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16
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Ding Y, Zhang R, Li B, Du Y, Li J, Tong X, Wu Y, Ji X, Zhang Y. Tissue distribution of polystyrene nanoplastics in mice and their entry, transport, and cytotoxicity to GES-1 cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 280:116974. [PMID: 33784569 DOI: 10.1016/j.envpol.2021.116974] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/12/2021] [Accepted: 03/16/2021] [Indexed: 05/14/2023]
Abstract
With the widespread use of plastics and nanotechnology products, nanoplastics (NPs) have become a potential threat to human health. It is of great practical significance to study and evaluate the distribution of NPs in mice as mammal models and their entry, transport, and cytotoxicity in human cell lines. In this study, we detected the tissue distribution of fluorescent polystyrene nanoplastics (PS-NPs) in mice and assessed their endocytosis, transport pathways, and cytotoxic effects in GES-1 cells. We found that PS-NPs were clearly visible in gastric, intestine, and liver tissues of mice and in GES-1 cells treated with PS-NPs. Entry of PS-NPs into GES-1 cells decreased with the inhibition of caveolae-mediated endocytosis (nystatin), clathrin-mediated endocytosis (chlorpromazine HCl), micropinocytosis (ethyl-isopropyl amiloride), RhoA (CCG-1423), and F-actin polymerization (lantrunculin A). Rac1 inhibitors (NSC 23766) had no significant effect on PS-NPs entering GES-1 cells. F-actin levels significantly decreased in CCG-1423-pretreated GES-1 cells exposed to PS-NPs. GES-1 cell ultrastructural features indicated that internalized PS-NPs can be encapsulated in vesicles, autophagosomes, lysosomes, and lysosomal residues. RhoA, F-actin, RAB7, and LAMP1 levels in PS-NPs-treated GES-1 cells were remarkably up-regulated and the Rab5 level was significantly down-regulated compared to levels in untreated cells. PS-NPs treatment decreased cell proliferation rates and increased cell apoptosis. The formation of autophagosomes and autolysosomes and levels of LC3II increased with the length of PS-NPs treatment. The results indicated that cells regulated endocytosis in response to PS-NPs through the RhoA/F-actin signaling pathway and internalized PS-NPs in the cytoplasm, autophagosomes, or lysosomes produced cytotoxicity. These results illustrate the potential threat of NPs pollution to human health.
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Affiliation(s)
- Yunfei Ding
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Ruiqing Zhang
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Boqing Li
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Yunqiu Du
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Jing Li
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Xiaohan Tong
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Yulong Wu
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Xiaofei Ji
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Ying Zhang
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, 264003, China.
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17
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Impairments of Photoreceptor Outer Segments Renewal and Phototransduction Due to a Peripherin Rare Haplotype Variant: Insights from Molecular Modeling. Int J Mol Sci 2021; 22:ijms22073484. [PMID: 33801777 PMCID: PMC8036374 DOI: 10.3390/ijms22073484] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Retinitis pigmentosa punctata albescens (RPA) is a particular form of retinitis pigmentosa characterized by childhood onset night blindness and areas of peripheral retinal atrophy. We investigated the genetic cause of RPA in a family consisting of two affected Egyptian brothers with healthy consanguineous parents. METHODS Mutational analysis of four RPA causative genes was realized by Sanger sequencing on both probands, and detected variants were subsequently genotyped in their parents. Afterwards, found variants were deeply, statistically, and in silico characterized to determine their possible effects and association with RPA. RESULTS Both brothers carry three missense PRPH2 variants in a homozygous condition (c.910C > A, c.929G > A, and c.1013A > C) and two promoter variants in RHO (c.-26A > G) and RLBP1 (c.-70G > A) genes, respectively. Haplotype analyses highlighted a PRPH2 rare haplotype variant (GAG), determining a possible alteration of PRPH2 binding with melanoregulin and other outer segment proteins, followed by photoreceptor outer segment instability. Furthermore, an altered balance of transcription factor binding sites, due to the presence of RHO and RLBP1 promoter variants, might determine a comprehensive downregulation of both genes, possibly altering the PRPH2 shared visual-related pathway. CONCLUSIONS Despite several limitations, the study might be a relevant step towards detection of novel scenarios in RPA etiopathogenesis.
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18
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Ma Z, Liu X, Nath S, Sun H, Tran TM, Yang L, Mayor S, Miao Y. Formin nanoclustering-mediated actin assembly during plant flagellin and DSF signaling. Cell Rep 2021; 34:108884. [PMID: 33789103 DOI: 10.1016/j.celrep.2021.108884] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/11/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Plants respond to bacterial infection acutely with actin remodeling during plant immune responses. The mechanisms by which bacterial virulence factors (VFs) modulate plant actin polymerization remain enigmatic. Here, we show that plant-type-I formin serves as the molecular sensor for actin remodeling in response to two bacterial VFs: Xanthomonas campestris pv. campestris (Xcc) diffusible signal factor (DSF), and pathogen-associated molecular pattern (PAMP) flagellin in pattern-triggered immunity (PTI). Both VFs regulate actin assembly by tuning the clustering and nucleation activity of formin on the plasma membrane (PM) at the nano-sized scale. By being integrated within the cell-wall-PM-actin cytoskeleton (CW-PM-AC) continuum, the dynamic behavior and function of formins are highly dependent on each scaffold layer's composition within the CW-PM-AC continuum during both DSF and PTI signaling. Our results reveal a central mechanism for rapid actin remodeling during plant-bacteria interactions, in which bacterial signaling molecules fine tune plant formin nanoclustering in a host mechanical-structure-dependent manner.
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Affiliation(s)
- Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xiaolin Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sangeeta Nath
- Institute for Stem Cell Biology and Regenerative Medicine, Bellary Road, Bangalore 560065, India; Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore 560065, India
| | - He Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tuan Minh Tran
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen 518055, China
| | - Satyajit Mayor
- Institute for Stem Cell Biology and Regenerative Medicine, Bellary Road, Bangalore 560065, India; National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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19
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Xie Y, Miao Y. Polarisome assembly mediates actin remodeling during polarized yeast and fungal growth. J Cell Sci 2021; 134:134/1/jcs247916. [PMID: 33419950 DOI: 10.1242/jcs.247916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dynamic assembly and remodeling of actin is critical for many cellular processes during development and stress adaptation. In filamentous fungi and budding yeast, actin cables align in a polarized manner along the mother-to-daughter cell axis, and are essential for the establishment and maintenance of polarity; moreover, they rapidly remodel in response to environmental cues to achieve an optimal system response. A formin at the tip region within a macromolecular complex, called the polarisome, is responsible for driving actin cable polymerization during polarity establishment. This polarisome undergoes dynamic assembly through spatial and temporally regulated interactions between its components. Understanding this process is important to comprehend the tuneable activities of the formin-centered nucleation core, which are regulated through divergent molecular interactions and assembly modes within the polarisome. In this Review, we focus on how intrinsically disordered regions (IDRs) orchestrate the condensation of the polarisome components and the dynamic assembly of the complex. In addition, we address how these components are dynamically distributed in and out of the assembly zone, thereby regulating polarized growth. We also discuss the potential mechanical feedback mechanisms by which the force-induced actin polymerization at the tip of the budding yeast regulates the assembly and function of the polarisome.
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Affiliation(s)
- Ying Xie
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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20
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Ma Z, Miao Y. Review: F-Actin remodelling during plant signal transduction via biomolecular assembly. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110663. [PMID: 33218630 DOI: 10.1016/j.plantsci.2020.110663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
During signal transduction, multivalent interactions establish dynamic molecular connectivities that propagate molecular cascades throughout the entire signaling pathway. Such multivalent interactions include the initial activation, cascade signal transduction, and the amplification and assembly of structural machinery. For example, plants rapidly remodel the actin cytoskeleton during signal transduction by perceiving a wide range of mechanical and chemical cues from developmental and defense pathways. Actin treadmilling is stepwise-regulated by interactions between actin and actin-binding proteins (ABPs). Emerging evidence shows that intrinsically disordered regions (IDRs) enable flexible and promiscuous interactions that serve as the functional hub for generating cellular interactomes underlying various signaling events. Though IDRs are present in a majority of ABPs, few of the functional roles of IDR in the interaction and functions of ABPs have been defined. The distinct features of IDRs create diverse and dynamic molecular interactions that introduce a new paradigm to our understanding of the structure-function relationships for actin assembly. In this review, we will create a snapshot of recent advances in IDR-mediated plant actin remodeling and discuss future research directions in studying the complexity of actin assembly via multifaceted biomolecular assembly during signal transduction.
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Affiliation(s)
- Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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21
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Chung D, Shum A, Caraveo G. GAP-43 and BASP1 in Axon Regeneration: Implications for the Treatment of Neurodegenerative Diseases. Front Cell Dev Biol 2020; 8:567537. [PMID: 33015061 PMCID: PMC7494789 DOI: 10.3389/fcell.2020.567537] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/14/2020] [Indexed: 01/06/2023] Open
Abstract
Growth-associated protein-43 (GAP-43) and brain acid-soluble protein 1 (BASP1) regulate actin dynamics and presynaptic vesicle cycling at axon terminals, thereby facilitating axonal growth, regeneration, and plasticity. These functions highly depend on changes in GAP-43 and BASP1 expression levels and post-translational modifications such as phosphorylation. Interestingly, examinations of GAP-43 and BASP1 in neurodegenerative diseases reveal alterations in their expression and phosphorylation profiles. This review provides an overview of the structural properties, regulations, and functions of GAP-43 and BASP1, highlighting their involvement in neural injury response and regeneration. By discussing GAP-43 and BASP1 in the context of neurodegenerative diseases, we also explore the therapeutic potential of modulating their activities to compensate for neuron loss in neurodegenerative diseases.
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Affiliation(s)
- Daayun Chung
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrew Shum
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Gabriela Caraveo
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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22
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Qiao Z, Sun H, Ng JTY, Ma Q, Koh SH, Mu Y, Miao Y, Gao YG. Structural and computational examination of the Arabidopsis profilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly. J Biol Chem 2019; 294:18650-18661. [PMID: 31653702 PMCID: PMC6901310 DOI: 10.1074/jbc.ra119.011307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/18/2019] [Indexed: 11/06/2022] Open
Abstract
Profilins are abundant cytosolic proteins that are universally expressed in eukaryotes and that regulate actin filament elongation by binding to both monomeric actin (G-actin) and formin proteins. The atypical profilin Arabidopsis AtPRF3 has been reported to cooperate with canonical profilin isoforms in suppressing formin-mediated actin polymerization during plant innate immunity responses. AtPRF3 has a 37-amino acid-long N-terminal extension (NTE), and its suppressive effect on actin assembly is derived from enhanced interaction with the polyproline (Poly-P) of the formin AtFH1. However, the molecular mechanism remains unclear. Here, we solved the crystal structures of AtPRF3Δ22 and AtPRF3Δ37, as well as AtPRF2 apo form and in complex with AtFH1 Poly-P at 1.5-3.6 Å resolutions. By combining these structures with molecular modeling, we found that AtPRF3Δ22 NTE has high plasticity, with a primary "closed" conformation that can adopt an open conformation that enables Poly-P binding. Furthermore, using molecular dynamics simulation and free-energy calculations of protein-protein binding, along with experimental validation, we show that the AtPRF3Δ22 binds to Poly-P in an adaptive manner, thereby enabling different binding modes that maintain the interaction through disordered sequences. Together, our structural and simulation results suggest that the dynamic conformational changes of the AtPRF3 NTE upon Poly-P binding modulate their interactions to fine-tune formin-mediated actin assembly.
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Affiliation(s)
- Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - He Sun
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Justin Tze Yang Ng
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Si Hui Koh
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore; School of Chemical and Biomedical Engineering, Nanyang Technological University, 637371 Singapore.
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore; Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 138673 Singapore; Nanyang Technological University Institute of Structural Biology, Nanyang Technological University, 639798 Singapore.
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23
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Söding J, Zwicker D, Sohrabi-Jahromi S, Boehning M, Kirschbaum J. Mechanisms for Active Regulation of Biomolecular Condensates. Trends Cell Biol 2019; 30:4-14. [PMID: 31753533 DOI: 10.1016/j.tcb.2019.10.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022]
Abstract
Liquid-liquid phase separation is a key organizational principle in eukaryotic cells, on par with intracellular membranes. It allows cells to concentrate specific proteins into condensates, increasing reaction rates and achieving switch-like regulation. We propose two active mechanisms that can explain how cells regulate condensate formation and size. In both, the cell regulates the activity of an enzyme, often a kinase, that adds post-translational modifications to condensate proteins. In enrichment inhibition, the enzyme enriches in the condensate and weakens interactions, as seen in stress granules (SGs), Cajal bodies, and P granules. In localization-induction, condensates form around immobilized enzymes that strengthen interactions, as observed in DNA repair, transmembrane signaling, and microtubule assembly. These models can guide studies into the many emerging roles of biomolecular condensates.
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Affiliation(s)
- Johannes Söding
- Quantitative Biology and Bioinformatics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany
| | - Salma Sohrabi-Jahromi
- Quantitative Biology and Bioinformatics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marc Boehning
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jan Kirschbaum
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany
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24
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Polarisome scaffolder Spa2-mediated macromolecular condensation of Aip5 for actin polymerization. Nat Commun 2019; 10:5078. [PMID: 31699995 PMCID: PMC6838200 DOI: 10.1038/s41467-019-13125-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/11/2019] [Indexed: 11/25/2022] Open
Abstract
A multiprotein complex polarisome nucleates actin cables for polarized cell growth in budding yeast and filamentous fungi. However, the dynamic regulations of polarisome proteins in polymerizing actin under physiological and stress conditions remains unknown. We identify a previously functionally unknown polarisome member, actin-interacting-protein 5 (Aip5), which promotes actin assembly synergistically with formin Bni1. Aip5-C terminus is responsible for its activities by interacting with G-actin and Bni1. Through N-terminal intrinsically disordered region, Aip5 forms high-order oligomers and generate cytoplasmic condensates under the stresses conditions. The molecular dynamics and reversibility of Aip5 condensates are regulated by scaffolding protein Spa2 via liquid-liquid phase separation both in vitro and in vivo. In the absence of Spa2, Aip5 condensates hamper cell growth and actin cable structures under stress treatment. The present study reveals the mechanisms of actin assembly for polarity establishment and the adaptation in stress conditions to protect actin assembly by protein phase separation. The polarisome is a dynamic protein complex that nucleates F-actin for polarized yeast growth, but its regulation is unclear. Here, the authors report that the polarisome protein Aip5 undergoes Spa2-mediated phase separation in physiological and stress conditions, potentially for regulating actin assembly.
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25
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The Control Centers of Biomolecular Phase Separation: How Membrane Surfaces, PTMs, and Active Processes Regulate Condensation. Mol Cell 2019; 76:295-305. [PMID: 31604601 DOI: 10.1016/j.molcel.2019.09.016] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022]
Abstract
Biomolecular condensation is emerging as an essential process for cellular compartmentalization. The formation of biomolecular condensates can be driven by liquid-liquid phase separation, which arises from weak, multivalent interactions among proteins and nucleic acids. A substantial body of recent work has revealed that diverse cellular processes rely on biomolecular condensation and that aberrant phase separation may cause disease. Many proteins display an intrinsic propensity to undergo phase separation. However, the mechanisms by which cells regulate phase separation to build functional condensates at the appropriate time and location are only beginning to be understood. Here, we review three key cellular mechanisms that enable the control of biomolecular phase separation: membrane surfaces, post-translational modifications, and active processes. We discuss how these mechanisms may function in concert to provide robust control over biomolecular condensates and suggest new research avenues that will elucidate how cells build and maintain these key centers of cellular compartmentalization.
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26
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Turoverov KK, Kuznetsova IM, Fonin AV, Darling AL, Zaslavsky BY, Uversky VN. Stochasticity of Biological Soft Matter: Emerging Concepts in Intrinsically Disordered Proteins and Biological Phase Separation. Trends Biochem Sci 2019; 44:716-728. [PMID: 31023505 DOI: 10.1016/j.tibs.2019.03.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022]
Abstract
At the turn of this century, cardinal changes took place in the perceptions of the structure and function of proteins, as well as in the organizational principles of membrane-less organelles. As a result, the model of the organization of living matter is changing to one described by highly dynamic biological soft matter positioned at the edge of chaos. Intrinsically disordered proteins (IDPs) and membrane-less organelles are key examples of this new outlook and may represent a critical foundation of life, defining its complexity and the evolution of living things.
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Affiliation(s)
- Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; Peter the Great St. Petersburg Polytechnic University, Department of Biophysics, Polytechnicheskaya Av. 29, St. Petersburg 195251, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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27
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Qian D, Xiang Y. Actin Cytoskeleton as Actor in Upstream and Downstream of Calcium Signaling in Plant Cells. Int J Mol Sci 2019; 20:ijms20061403. [PMID: 30897737 PMCID: PMC6471457 DOI: 10.3390/ijms20061403] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 01/04/2023] Open
Abstract
In plant cells, calcium (Ca2+) serves as a versatile intracellular messenger, participating in several fundamental and important biological processes. Recent studies have shown that the actin cytoskeleton is not only an upstream regulator of Ca2+ signaling, but also a downstream regulator. Ca2+ has been shown to regulates actin dynamics and rearrangements via different mechanisms in plants, and on this basis, the upstream signaling encoded within the Ca2+ transient can be decoded. Moreover, actin dynamics have also been proposed to act as an upstream of Ca2+, adjust Ca2+ oscillations, and establish cytosolic Ca2+ ([Ca2+]cyt) gradients in plant cells. In the current review, we focus on the advances in uncovering the relationship between the actin cytoskeleton and calcium in plant cells and summarize our current understanding of this relationship.
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Affiliation(s)
- Dong Qian
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Yun Xiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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28
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Lacy MM, Ma R, Ravindra NG, Berro J. Molecular mechanisms of force production in clathrin-mediated endocytosis. FEBS Lett 2018; 592:3586-3605. [PMID: 30006986 PMCID: PMC6231980 DOI: 10.1002/1873-3468.13192] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/21/2018] [Accepted: 07/12/2018] [Indexed: 01/21/2023]
Abstract
During clathrin-mediated endocytosis (CME), a flat patch of membrane is invaginated and pinched off to release a vesicle into the cytoplasm. In yeast CME, over 60 proteins-including a dynamic actin meshwork-self-assemble to deform the plasma membrane. Several models have been proposed for how actin and other molecules produce the forces necessary to overcome the mechanical barriers of membrane tension and turgor pressure, but the precise mechanisms and a full picture of their interplay are still not clear. In this review, we discuss the evidence for these force production models from a quantitative perspective and propose future directions for experimental and theoretical work that could clarify their various contributions.
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Affiliation(s)
- Michael M Lacy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, USA
| | - Rui Ma
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Neal G Ravindra
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, USA
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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