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Su B, Wang A, Xie D, Shan X. VA-TIRFM-based SM kymograph analysis for dwell time and colocalization of plasma membrane protein in plant cells. PLANT METHODS 2023; 19:70. [PMID: 37422677 DOI: 10.1186/s13007-023-01047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND The plasma membrane (PM) proteins function in a highly dynamic state, including protein trafficking and protein homeostasis, to regulate various biological processes. The dwell time and colocalization of PM proteins are considered to be two important dynamic features determining endocytosis and protein interactions, respectively. Dwell-time and colocalization detected using traditional fluorescence microscope techniques are often misestimated due to bulk measurement. In particular, analyzing these two features of PM proteins at the single-molecule level with spatiotemporal continuity in plant cells remains greatly challenging. RESULTS We developed a single molecular (SM) kymograph method, which is based on variable angle-total internal reflection fluorescence microscopy (VA-TIRFM) observation and single-particle (co-)tracking (SPT) analysis, to accurately analyze the dwell time and colocalization of PM proteins in a spatial and temporal manner. Furthermore, we selected two PM proteins with distinct dynamic behaviors, including AtRGS1 (Arabidopsis regulator of G protein signaling 1) and AtREM1.3 (Arabidopsis remorin 1.3), to analyze their dwell time and colocalization upon jasmonate (JA) treatment by SM kymography. First, we established new 3D (2D+t) images to view all trajectories of the interest protein by rotating these images, and then we chose the appropriate point without changing the trajectory for further analysis. Upon JA treatment, the path lines of AtRGS1-YFP appeared curved and short, while the horizontal lines of mCherry-AtREM1.3 demonstrated limited changes, indicating that JA might initiate the endocytosis of AtRGS1. Analysis of transgenic seedlings coexpressing AtRGS1-YFP/mCherry-AtREM1.3 revealed that JA induces a change in the trajectory of AtRGS1-YFP, which then merges into the kymography line of mCherry-AtREM1.3, implying that JA increases the colocalization degree between AtRGS1 and AtREM1.3 on the PM. These results illustrate that different types of PM proteins exhibit specific dynamic features in line with their corresponding functions. CONCLUSIONS The SM-kymograph method provides new insight into quantitively analyzing the dwell time and correlation degree of PM proteins at the single-molecule level in living plant cells.
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Affiliation(s)
- Bodan Su
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Anqi Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Daoxin Xie
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaoyi Shan
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, and School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Ding J, Li X, Shen J, Zhao Y, Zhong S, Lai L, Niu H, Qi Z. ssDNA accessibility of Rad51 is regulated by orchestrating multiple RPA dynamics. Nat Commun 2023; 14:3864. [PMID: 37391417 PMCID: PMC10313831 DOI: 10.1038/s41467-023-39579-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
The eukaryotic single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA) plays a crucial role in various DNA metabolic pathways, including DNA replication and repair, by dynamically associating with ssDNA. While the binding of a single RPA molecule to ssDNA has been thoroughly studied, the accessibility of ssDNA is largely governed by the bimolecular behavior of RPA, the biophysical nature of which remains unclear. In this study, we develop a three-step low-complexity ssDNA Curtains method, which, when combined with biochemical assays and a Markov chain model in non-equilibrium physics, allow us to decipher the dynamics of multiple RPA binding to long ssDNA. Interestingly, our results suggest that Rad52, the mediator protein, can modulate the ssDNA accessibility of Rad51, which is nucleated on RPA coated ssDNA through dynamic ssDNA exposure between neighboring RPA molecules. We find that this process is controlled by the shifting between the protection mode and action mode of RPA ssDNA binding, where tighter RPA spacing and lower ssDNA accessibility are favored under RPA protection mode, which can be facilitated by the Rfa2 WH domain and inhibited by Rad52 RPA interaction.
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Affiliation(s)
- Jiawei Ding
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, CA, USA
| | - Jiangchuan Shen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Yiling Zhao
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shuchen Zhong
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Single-Molecule Imaging in Living Plant Cells: A Methodological Review. Int J Mol Sci 2021; 22:ijms22105071. [PMID: 34064786 PMCID: PMC8151321 DOI: 10.3390/ijms22105071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging is emerging as a revolutionary approach to studying fundamental questions in plants. However, compared with its use in animals, the application of single-molecule imaging in plants is still underexplored. Here, we review the applications, advantages, and challenges of single-molecule fluorescence imaging in plant systems from the perspective of methodology. Firstly, we provide a general overview of single-molecule imaging methods and their principles. Next, we summarize the unprecedented quantitative details that can be obtained using single-molecule techniques compared to bulk assays. Finally, we discuss the main problems encountered at this stage and provide possible solutions.
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Lv X, Wu Y, Tian R, Gu Y, Liu Y, Li J, Du G, Ledesma-Amaro R, Liu L. Synthetic metabolic channel by functional membrane microdomains for compartmentalized flux control. Metab Eng 2020; 59:106-118. [DOI: 10.1016/j.ymben.2020.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
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Single-Molecule Imaging and Computational Microscopy Approaches Clarify the Mechanism of the Dimerization and Membrane Interactions of Green Fluorescent Protein. Int J Mol Sci 2019; 20:ijms20061410. [PMID: 30897814 PMCID: PMC6471090 DOI: 10.3390/ijms20061410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 02/01/2023] Open
Abstract
Green fluorescent protein (GFP) is widely used as a biomarker in living systems; however, GFP and its variants are prone to forming low-affinity dimers under physiological conditions. This undesirable tendency is exacerbated when fluorescent proteins (FP) are confined to membranes, fused to naturally-oligomeric proteins, or expressed at high levels in cells. Oligomerization of FPs introduces artifacts into the measurement of subunit stoichiometry, as well as interactions between proteins fused to FPs. Introduction of a single mutation, A206K, has been shown to disrupt hydrophobic interactions in the region responsible for GFP dimerization, thereby contributing to its monomerization. Nevertheless, a detailed understanding of how this single amino acid-dependent inhibition of dimerization in GFP occurs at the atomic level is still lacking. Single-molecule experiments combined with computational microscopy (atomistic molecular dynamics) revealed that the amino group of A206 contributes to GFP dimer formation via a multivalent electrostatic interaction. We further showed that myristoyl modification is an efficient mechanism to promote membrane attachment of GFP. Molecular dynamics-based site-directed mutagenesis has been used to identify the key functional residues in FPs. The data presented here have been utilized as a monomeric control in downstream single-molecule studies, facilitating more accurate stoichiometry quantification of functional protein complexes in living cells.
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Cui Y, Yu M, Yao X, Xing J, Lin J, Li X. Single-Particle Tracking for the Quantification of Membrane Protein Dynamics in Living Plant Cells. MOLECULAR PLANT 2018; 11:1315-1327. [PMID: 30296600 DOI: 10.1016/j.molp.2018.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 05/25/2023]
Abstract
The plasma membrane is a sophisticated, organized, and highly heterogeneous structure that compartmentalizes cellular processes. To decipher the biological processes involving membrane proteins, it is necessary to analyze their spatiotemporal dynamics. However, it is difficult to directly assess the dynamics and interactions of biomolecules in living cells using traditional biochemical methods. Single-particle tracking (SPT) methods for imaging and tracking single particles conjugated with fluorescent probes offer an ideal approach to acquire valuable and complementary information about dynamic intracellular processes. SPT can be used to quantitatively monitor the diverse motions of individual particles in living cells. SPT also provides super-spatiotemporal resolution that allows early-stage or rapid response information to be obtained for a better understanding of molecular basis of associated signal transduction processes. More importantly, SPT can be used to detect the motion paths of individual biomolecules in vivo and in situ, thus unveiling the dynamic behavior of the biomolecules that support developmental processes in living cells. In this review, we give an overview of SPT methods, from image acquisition to the detection of single particles, as well as tracking and data analysis. We also discuss recent applications of SPT methods in the field of plant biology to reveal the complex biological functions of membrane proteins.
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Affiliation(s)
- Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaomin Yao
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jingjing Xing
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Jinming Street, Kaifeng 475001, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China.
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Xue Y, Xing J, Wan Y, Lv X, Fan L, Zhang Y, Song K, Wang L, Wang X, Deng X, Baluška F, Christie JM, Lin J. Arabidopsis Blue Light Receptor Phototropin 1 Undergoes Blue Light-Induced Activation in Membrane Microdomains. MOLECULAR PLANT 2018; 11:846-859. [PMID: 29689384 DOI: 10.1016/j.molp.2018.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 02/26/2018] [Accepted: 04/02/2018] [Indexed: 05/06/2023]
Abstract
Phototropin (phot)-mediated signaling initiated by blue light (BL) plays a critical role in optimizing photosynthetic light capture at the plasma membrane (PM) in plants. However, the mechanisms underlying the regulation of phot activity at the PM in response to BL remain largely unclear. In this study, by single-particle tracking and stepwise photobleaching analysis of phot1-GFP proteins we demonstrated that in the dark phot1 proteins remain in an inactive state and mostly exist as monomers. Dimerization and the diffusion rate of phot1-GFP increased in a dose-dependent manner in response to BL. In contrast, BL did not affect the lateral diffusion of kinase-inactive phot1D806N-GFP but did enhance its dimerization, suggesting that phot1 dimerization is independent of phosphorylation. Förster resonance energy transfer-fluorescence lifetime imaging microscopy analysis revealed that the interaction between phot1-GFP and a marker of sterol-rich lipid environments, AtRem1.3-mCherry, was enhanced with increased time of BL treatment. However, this BL-dependent interaction was not obvious in plants co-expressing phot1D806N-GFP and AtRem1.3-mCherry, indicating that BL facilitates the translocation of functional phot1-GFP into AtRem1.3-labeled microdomains to activate phot-mediated signaling. Conversely, sterol depletion attenuated phot1-GFP dynamics, dimerization, and phosphorylation. Taken together, these results indicate that membrane microdomains act as organizing platforms essential for the proper function of activated phot1 at the PM.
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Affiliation(s)
- Yiqun Xue
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingjing Xing
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinglang Wan
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xueqin Lv
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lusheng Fan
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kai Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaohua Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin Deng
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, 53115 Bonn, Germany
| | - John M Christie
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Jinxing Lin
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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Wang L, Xue Y, Xing J, Song K, Lin J. Exploring the Spatiotemporal Organization of Membrane Proteins in Living Plant Cells. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:525-551. [PMID: 29489393 DOI: 10.1146/annurev-arplant-042817-040233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plasma membrane proteins have important roles in transport and signal transduction. Deciphering the spatiotemporal organization of these proteins provides crucial information for elucidating the links between the behaviors of different molecules. However, monitoring membrane proteins without disrupting their membrane environment remains difficult. Over the past decade, many studies have developed single-molecule techniques, opening avenues for probing the stoichiometry and interactions of membrane proteins in their native environment by providing nanometer-scale spatial information and nanosecond-scale temporal information. In this review, we assess recent progress in the development of labeling and imaging technology for membrane protein analysis. We focus in particular on several single-molecule techniques for quantifying the dynamics and assembly of membrane proteins. Finally, we provide examples of how these new techniques are advancing our understanding of the complex biological functions of membrane proteins.
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Affiliation(s)
- Li Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Yiqun Xue
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingjing Xing
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kai Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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