1
|
Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 DOI: 10.1007/s41061-024-00455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
Collapse
Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| |
Collapse
|
2
|
Işık M, Kısaçam MA. Readily Accessible and Brightly Fluorogenic BODIPY/NBD-Tetrazines via S NAr Reactions. J Org Chem 2024; 89:6513-6519. [PMID: 38598957 PMCID: PMC11077493 DOI: 10.1021/acs.joc.3c02864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024]
Abstract
We describe SNAr reactions of some commercial amino-tetrazines and halo-dyes, which give efficiently quenched BODIPY/NBD-tetrazines (ΦFl < 0.01) in high yields and, importantly, with high purities affordable via simple silica gel chromatography only. The dyes exhibit large Stokes shifts, moderate environmental sensitivity, and emission enhancements (up to 193-fold) upon Tz ligation with BCN─a strained dienophile. They successfully serve as labels for HSA protein premodified with BCN, resulting in bright blue-green emission upon ligation.
Collapse
Affiliation(s)
- Murat Işık
- Department
of Food Engineering, Bingöl University, 12000 Bingöl, Türkiye
| | - Mehmet Ali Kısaçam
- Department
of Biochemistry, Faculty of Veterinary Medicine, Mustafa Kemal University, 31060 Hatay, Türkiye
| |
Collapse
|
3
|
Huang W, Laughlin ST. Cell-selective bioorthogonal labeling. Cell Chem Biol 2024; 31:409-427. [PMID: 37837964 DOI: 10.1016/j.chembiol.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/25/2023] [Accepted: 09/19/2023] [Indexed: 10/16/2023]
Abstract
In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.
Collapse
Affiliation(s)
- Wei Huang
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Scott T Laughlin
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
4
|
Jamecna D, Höglinger D. The use of click chemistry in sphingolipid research. J Cell Sci 2024; 137:jcs261388. [PMID: 38488070 DOI: 10.1242/jcs.261388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Sphingolipid dysregulation is involved in a range of rare and fatal diseases as well as common pathologies including cancer, infectious diseases or neurodegeneration. Gaining insights into how sphingolipids are involved in these diseases would contribute much to our understanding of human physiology, as well as the pathology mechanisms. However, scientific progress is hampered by a lack of suitable tools that can be used in intact systems. To overcome this, efforts have turned to engineering modified lipids with small clickable tags and to harnessing the power of click chemistry to localize and follow these minimally modified lipid probes in cells. We hope to inspire the readers of this Review to consider applying existing click chemistry tools for their own aspects of sphingolipid research. To this end, we focus here on different biological applications of clickable lipids, mainly to follow metabolic conversions, their visualization by confocal or superresolution microscopy or the identification of their protein interaction partners. Finally, we describe recent approaches employing organelle-targeted and clickable lipid probes to accurately follow intracellular sphingolipid transport with organellar precision.
Collapse
Affiliation(s)
- Denisa Jamecna
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69118 Heidelberg, Germany
| | - Doris Höglinger
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69118 Heidelberg, Germany
| |
Collapse
|
5
|
Zheng S, Dadina N, Mozumdar D, Lesiak L, Martinez KN, Miller EW, Schepartz A. Long-term super-resolution inner mitochondrial membrane imaging with a lipid probe. Nat Chem Biol 2024; 20:83-92. [PMID: 37857992 PMCID: PMC10746544 DOI: 10.1038/s41589-023-01450-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
The inner mitochondrial membrane (IMM) generates power to drive cell function, and its dynamics control mitochondrial health and cellular homeostasis. Here, we describe the cell-permeant, lipid-like small molecule MAO-N3 and use it to assemble high-density environmentally sensitive (HIDE) probes that selectively label and image the IMM in live cells and multiple cell states. MAO-N3 pairs with strain-promoted azide-alkyne click chemistry-reactive fluorophores to support HIDE imaging using confocal, structured illumination, single-molecule localization and stimulated emission depletion microscopy, all with significantly improved resistance to photobleaching. These probes generate images with excellent spatial and temporal resolution, require no genetic manipulations, are non-toxic in model cell lines and primary cardiomyocytes (even under conditions that amplify the effects of mitochondrial toxins) and can visualize mitochondrial dynamics for 12.5 h. This probe will enable comprehensive studies of IMM dynamics with high temporal and spatial resolution.
Collapse
Affiliation(s)
- Shuai Zheng
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Neville Dadina
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Deepto Mozumdar
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Lauren Lesiak
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Kayli N Martinez
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
6
|
Chen Y, Hao T, Wang J, Chen Y, Wang X, Wei W, Zhao J, Qian Y. A Near-Infrared Fluorogenic Probe for Rapid, Specific, and Ultrasensitive Detection of Sphingosine in Living Cells and In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307598. [PMID: 38032131 PMCID: PMC10787105 DOI: 10.1002/advs.202307598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Sphingosine (Sph) plays important roles in various complex biological processes. Abnormalities in Sph metabolism can result in various diseases, including neurodegenerative disorders. However, due to the lack of rapid and accurate detection methods, understanding sph metabolic in related diseases is limited. Herein, a series of near-infrared fluorogenic probes DMS-X (X = 2F, F, Cl, Br, and I) are designed and synthesized. The fast oxazolidinone ring formation enables the DMS-2F to detect Sph selectively and ultrasensitively, and the detection limit reaches 9.33 ± 0.41 nm. Moreover, it is demonstrated that DMS-2F exhibited a dose- and time-dependent response to Sph and can detect sph in living cells. Importantly, for the first time, the changes in Sph levels induced by Aβ42 oligomers and H2 O2 are assessed through a fluorescent imaging approach, and further validated the physiological processes by which Aβ42 oligomers and reactive oxygen species (ROS)-induce changes in intracellular Sph levels. Additionally, the distribution of Sph in living zebrafish is successfully mapped by in vivo imaging of a zebrafish model. This work provides a simple and efficient method for probing Sph in living cells and in vivo, which will facilitate investigation into the metabolic process of Sph and the connection between Sph and disease pathologies.
Collapse
Affiliation(s)
- Yanyan Chen
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Tingting Hao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jing Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yiming Chen
- School of Engineering, Vanderbilt University, Nashville, 37235, USA
| | - Xiuxiu Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei Wei
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yong Qian
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| |
Collapse
|
7
|
Šlachtová V, Chovanec M, Rahm M, Vrabel M. Bioorthogonal Chemistry in Cellular Organelles. Top Curr Chem (Cham) 2023; 382:2. [PMID: 38103067 PMCID: PMC10725395 DOI: 10.1007/s41061-023-00446-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/12/2023] [Indexed: 12/17/2023]
Abstract
While bioorthogonal reactions are routinely employed in living cells and organisms, their application within individual organelles remains limited. In this review, we highlight diverse examples of bioorthogonal reactions used to investigate the roles of biomolecules and biological processes as well as advanced imaging techniques within cellular organelles. These innovations hold great promise for therapeutic interventions in personalized medicine and precision therapies. We also address existing challenges related to the selectivity and trafficking of subcellular dynamics. Organelle-targeted bioorthogonal reactions have the potential to significantly advance our understanding of cellular organization and function, provide new pathways for basic research and clinical applications, and shape the direction of cell biology and medical research.
Collapse
Affiliation(s)
- Veronika Šlachtová
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
| | - Marek Chovanec
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Michal Rahm
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Milan Vrabel
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic.
| |
Collapse
|
8
|
Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
Collapse
Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
9
|
Si D, Li Q, Bao Y, Zhang J, Wang L. Fluorogenic and Cell-Permeable Rhodamine Dyes for High-Contrast Live-Cell Protein Labeling in Bioimaging and Biosensing. Angew Chem Int Ed Engl 2023; 62:e202307641. [PMID: 37483077 DOI: 10.1002/anie.202307641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
The advancement of fluorescence microscopy techniques has opened up new opportunities for visualizing proteins and unraveling their functions in living biological systems. Small-molecule organic dyes, which possess exceptional photophysical properties, small size, and high photostability, serve as powerful fluorescent reporters in protein imaging. However, achieving high-contrast live-cell labeling of target proteins with conventional organic dyes remains a considerable challenge in bioimaging and biosensing due to their inadequate cell permeability and high background signal. Over the past decade, a novel generation of fluorogenic and cell-permeable dyes has been developed, which have substantially improved live-cell protein labeling by fine-tuning the reversible equilibrium between a cell-permeable, nonfluorescent spirocyclic state (unbound) and a fluorescent zwitterion (protein-bound) of rhodamines. In this review, we present the mechanism and design strategies of these fluorogenic and cell-permeable rhodamines, as well as their applications in bioimaging and biosensing.
Collapse
Affiliation(s)
- Dongjuan Si
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Quanlin Li
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Yifan Bao
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Jingye Zhang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Lu Wang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| |
Collapse
|
10
|
Du Z, Wang W, Luo S, Zhang L, Yuan S, Hei Y, Bao Z, Chen C, Lin Y, Chu L. Self-Renewable Tag for Photostable Fluorescence Imaging of Proteins. J Am Chem Soc 2023; 145:18968-18976. [PMID: 37596976 DOI: 10.1021/jacs.3c06102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
We report the development of a self-renewable tag (srTAG) for protein fluorescence imaging. srTAG leverages the "on-protein" fluorophore equilibrium between the fluorescent zwitterion and non-fluorescent spirocyclic form and the reversible fluorescence labeling to enable self-recovery of fluorescence after photobleaching. This small-sized srTAG allows 2-6 times longer imaging duration compared to other commonly used self-labeling tags and is compatible with fluorophores with different spectral properties. This study provides a new strategy for fine tuning of self-labeling tags.
Collapse
Affiliation(s)
- Zhichao Du
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Wenjing Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Siyuan Luo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Lingjie Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuowei Yuan
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yongzhen Hei
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Zhangbin Bao
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, Beijing 100084, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Yi Lin
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, Beijing 100084, China
| | - Ling Chu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
11
|
Kozma E, Bojtár M, Kele P. Bioorthogonally Assisted Phototherapy: Recent Advances and Prospects. Angew Chem Int Ed Engl 2023; 62:e202303198. [PMID: 37161824 DOI: 10.1002/anie.202303198] [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: 03/03/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
Photoresponsive materials offer excellent spatiotemporal control over biological processes and the emerging phototherapeutic methods are expected to have significant effects on targeted cancer therapies. Recent examples show that combination of photoactivatable approaches with bioorthogonal chemistry enhances the precision of targeted phototherapies and profound implications are foreseen particularly in the treatment of disperse/diffuse tumors. The extra level of on-target selectivity and improved spatial/temporal control considerably intensified related bioorthogonally assisted phototherapy research. The anticipated growth of further developments in the field justifies the timeliness of a brief summary of the state of the art.
Collapse
Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Márton Bojtár
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| |
Collapse
|
12
|
Sarmento MJ, Llorente A, Petan T, Khnykin D, Popa I, Nikolac Perkovic M, Konjevod M, Jaganjac M. The expanding organelle lipidomes: current knowledge and challenges. Cell Mol Life Sci 2023; 80:237. [PMID: 37530856 PMCID: PMC10397142 DOI: 10.1007/s00018-023-04889-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lipids in cell membranes and subcellular compartments play essential roles in numerous cellular processes, such as energy production, cell signaling and inflammation. A specific organelle lipidome is characterized by lipid synthesis and metabolism, intracellular trafficking, and lipid homeostasis in the organelle. Over the years, considerable effort has been directed to the identification of the lipid fingerprints of cellular organelles. However, these fingerprints are not fully characterized due to the large variety and structural complexity of lipids and the great variability in the abundance of different lipid species. The process becomes even more challenging when considering that the lipidome differs in health and disease contexts. This review summarizes the information available on the lipid composition of mammalian cell organelles, particularly the lipidome of the nucleus, mitochondrion, endoplasmic reticulum, Golgi apparatus, plasma membrane and organelles in the endocytic pathway. The lipid compositions of extracellular vesicles and lamellar bodies are also described. In addition, several examples of subcellular lipidome dynamics under physiological and pathological conditions are presented. Finally, challenges in mapping organelle lipidomes are discussed.
Collapse
Affiliation(s)
- Maria J Sarmento
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, 0167, Oslo, Norway
- Faculty of Medicine, Centre for Cancer Cell Reprogramming, University of Oslo, Montebello, 0379, Oslo, Norway
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Iuliana Popa
- Pharmacy Department, Bâtiment Henri Moissan, University Paris-Saclay, 17 Avenue des Sciences, 91400, Orsay, France
| | | | - Marcela Konjevod
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Morana Jaganjac
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia.
| |
Collapse
|
13
|
Sawada S, Yoshikawa M, Tsutsui K, Miyazaki T, Kano K, Mishiro-Sato E, Tsukiji S. Palmitoylation-Dependent Small-Molecule Fluorescent Probes for Live-Cell Golgi Imaging. ACS Chem Biol 2023; 18:1047-1053. [PMID: 37098188 DOI: 10.1021/acschembio.3c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Small-molecule fluorescent probes enabling visualization of the Golgi apparatus in living cells are essential tools for studying Golgi-associated biological processes and diseases. So far, several fluorescent Golgi stains have been developed by linking ceramide lipids to fluorophores. However, ceramide-based probes suffer from cumbersome staining procedures and low Golgi specificity. Here, we introduce fluorescent Golgi-staining probes based on the tri-N-methylated myristoyl-Gly-Cys (myrGC3Me) motif. The cell-permeable myrGC3Me motif localizes to the Golgi membrane upon S-palmitoylation. By modularly conjugating the myrGC3Me motif to fluorophores, we developed blue, green, and red fluorescent Golgi probes, all of which allowed simple and rapid staining of the Golgi in living cells with high specificity and no cytotoxicity. The probe was also applicable to the visualization of dynamic changes of the Golgi morphology induced by drug treatments and during cell division. The present work provides an entirely new series of live-cell Golgi probes useful for cell biological and diagnostic applications.
Collapse
Affiliation(s)
- Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Keita Tsutsui
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Tomoki Miyazaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Keiko Kano
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8602, Japan
| | - Emi Mishiro-Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| |
Collapse
|
14
|
Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
Collapse
Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
15
|
Izquierdo E, López-Corrales M, Abad-Montero D, Rovira A, Fabriàs G, Bosch M, Abad JL, Marchán V. Fluorescently Labeled Ceramides and 1-Deoxyceramides: Synthesis, Characterization, and Cellular Distribution Studies. J Org Chem 2022; 87:16351-16367. [PMID: 36441972 PMCID: PMC9764360 DOI: 10.1021/acs.joc.2c02019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ceramides (Cer) are bioactive sphingolipids that have been proposed as potential disease biomarkers since they are involved in several cellular stress responses, including apoptosis and senescence. 1-Deoxyceramides (1-deoxyCer), a particular subtype of noncanonical sphingolipids, have been linked to the pathogenesis of type II diabetes. To investigate the metabolism of these bioactive lipids, as well as to have a better understanding of the signaling processes where they participate, it is essential to expand the toolbox of fluorescent sphingolipid probes exhibiting complementary subcellular localization. Herein, we describe a series of new sphingolipid probes tagged with two different organic fluorophores, a far-red/NIR-emitting coumarin derivative (COUPY) and a green-emitting BODIPY. The assembly of the probes involved a combination of olefin cross metathesis and click chemistry reactions as key steps, and these fluorescent ceramide analogues exhibited excellent emission quantum yields, being the Stokes' shifts of the COUPY derivatives much higher than those of the BODIPY counterparts. Confocal microscopy studies in HeLa cells confirmed an excellent cellular permeability for these sphingolipid probes and revealed that most of the vesicles stained by COUPY probes were either lysosomes or endosomes, whereas BODIPY probes accumulated either in Golgi apparatus or in nonlysosomal intracellular vesicles. The fact that the two sets of fluorescent Cer probes have such different staining patterns indicates that their subcellular distribution is not entirely defined by the sphingolipid moiety but rather influenced by the fluorophore.
Collapse
Affiliation(s)
- Eduardo Izquierdo
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Orgànica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028Barcelona, Spain
| | - Marta López-Corrales
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Orgànica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028Barcelona, Spain
| | - Diego Abad-Montero
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Orgànica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028Barcelona, Spain,Research
Unit on BioActive Molecules, Departament de Química Biològica, Institut de Química Avançada de Catalunya
(IQAC-CSIC), Jordi Girona
18-26, 08034Barcelona, Spain
| | - Anna Rovira
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Orgànica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028Barcelona, Spain
| | - Gemma Fabriàs
- Research
Unit on BioActive Molecules, Departament de Química Biològica, Institut de Química Avançada de Catalunya
(IQAC-CSIC), Jordi Girona
18-26, 08034Barcelona, Spain
| | - Manel Bosch
- Unitat
de Microscòpia Òptica Avanc̨ada, Centres Científics
i Tecnològics, Universitat de Barcelona
(UB), Av. Diagonal, 643, 08028Barcelona, Spain
| | - José Luís Abad
- Research
Unit on BioActive Molecules, Departament de Química Biològica, Institut de Química Avançada de Catalunya
(IQAC-CSIC), Jordi Girona
18-26, 08034Barcelona, Spain,
| | - Vicente Marchán
- Departament
de Química Inorgànica i Orgànica, Secció
de Química Orgànica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028Barcelona, Spain,Institut
de Biomedicina de la Universitat de Barcelona (IBUB), 08028Barcelona, Spain,
| |
Collapse
|
16
|
Dorn RS, Prescher JA. Bioorthogonal Phosphines: Then and Now. Isr J Chem 2022. [DOI: 10.1002/ijch.202200070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert S. Dorn
- Departments of Chemistry University of California Irvine California 92697 United States
| | - Jennifer A. Prescher
- Departments of Chemistry University of California Irvine California 92697 United States
- Molecular Biology & Biochemistry University of California Irvine California 92697 United States
- Pharmaceutical Sciences University of California Irvine California 92697 United States
| |
Collapse
|
17
|
Klier PEZ, Roo R, Miller EW. Fluorescent indicators for imaging membrane potential of organelles. Curr Opin Chem Biol 2022; 71:102203. [PMID: 36084425 PMCID: PMC10259174 DOI: 10.1016/j.cbpa.2022.102203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023]
Abstract
Plasma membrane potential is a key driver of the physiology of excitable cells like neurons and cardiomyocytes. Voltage-sensitive fluorescent indicators offer a powerful complement to traditional electrode-based approaches to measuring and monitoring membrane potential. Intracellular organelles can also generate membrane potential, yet the electrode- and fluorescent indicator-based approaches used for plasma membrane potential imaging are difficult to implement on intact organelles in their native environment. Here, we survey recent advances in developing and deploying voltage-sensitive fluorescent indicators to interrogate organelle membrane potential in intact cells.
Collapse
Affiliation(s)
- Pavel E Z Klier
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Ryan Roo
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA; Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
18
|
Lu Y, Zhu D, Le Q, Wang Y, Wang W. Ruthenium-based antitumor drugs and delivery systems from monotherapy to combination therapy. NANOSCALE 2022; 14:16339-16375. [PMID: 36341705 DOI: 10.1039/d2nr02994d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ruthenium complex is an important compound group for antitumor drug research and development. NAMI-A, KP1019, TLD1433 and other ruthenium complexes have entered clinical research. In recent years, the research on ruthenium antitumor drugs has not been limited to single chemotherapy drugs; other applications of ruthenium complexes have emerged such as in combination therapy. During the development of ruthenium complexes, drug delivery forms of ruthenium antitumor drugs have also evolved from single-molecule drugs to nanodrug delivery systems. The review summarizes the following aspects: (1) ruthenium complexes from monotherapy to combination therapy, including the development of single-molecule compounds, carrier nanomedicine, and self-assembly of carrier-free nanomedicine; (2) ruthenium complexes in the process of ADME in terms of absorption, distribution, metabolism and excretion; (3) the applications of ruthenium complexes in combination therapy, including photodynamic therapy (PDT), photothermal therapy (PTT), photoactivated chemotherapy (PACT), immunotherapy, and their combined application; (4) the future prospects of ruthenium-based antitumor drugs.
Collapse
Affiliation(s)
- Yu Lu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China.
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing Laboratory of Oral Health, Beijing 100069, P. R. China
- Department of Chemistry, University of Bergen, P. O. Box 7803, 5020 Bergen, Norway
| | - Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China.
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing Laboratory of Oral Health, Beijing 100069, P. R. China
| | - Quynh Le
- Center for Pharmacy, University of Bergen, P. O. Box 7803, 5020 Bergen, Norway.
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China.
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing Laboratory of Oral Health, Beijing 100069, P. R. China
| | - Wei Wang
- Center for Pharmacy, University of Bergen, P. O. Box 7803, 5020 Bergen, Norway.
- Department of Chemistry, University of Bergen, P. O. Box 7803, 5020 Bergen, Norway
| |
Collapse
|
19
|
Li RS, Wen C, Huang CZ, Li N. Functional molecules and nano-materials for the Golgi apparatus-targeted imaging and therapy. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
20
|
Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJC, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid—a Naturally Occurring 1,2‐Cyclopropene Fatty Acid—by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates**. Angew Chem Int Ed Engl 2022; 61:e202207640. [PMID: 35838324 PMCID: PMC9546306 DOI: 10.1002/anie.202207640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Indexed: 12/25/2022]
Abstract
In the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable pendant groups. To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2‐cyclopropene‐containing oleic acid analogue, as a bioorthogonal probe. We show that this lipid can be readily taken up by dendritic cells without toxic side effects, and that it can subsequently be visualised using an inverse electron‐demand Diels–Alder reaction with quenched tetrazine‐fluorophore conjugates. In addition, the lipid can be used to identify changes in protein oleoylation after immune cell activation. Finally, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper‐catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging.
Collapse
Affiliation(s)
- Kristine Bertheussen
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Merel van de Plassche
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Iakovia Ttofi
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alexi J. C. Sarris
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Sander I. van Kasteren
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
21
|
Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJ, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid – a Naturally Occurring 1,2‐Cyclopropene Fatty Acid – by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kristine Bertheussen
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | | | - Thomas Bakkum
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Berend Gagestein
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Iakovia Ttofi
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Alexi J.C. Sarris
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Herman S. Overkleeft
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Mario van der Stelt
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Sander Izaak van Kasteren
- Leiden University Leiden Institute of Chemistry Gorlaeus LaboratoryEinsteinweg 55 2333 CC Leiden NETHERLANDS
| |
Collapse
|
22
|
Kundu S, Das S, Jaiswal S, Patra A. Molecular to Supramolecular Self-Assembled Luminogens for Tracking the Intracellular Organelle Dynamics. ACS APPLIED BIO MATERIALS 2022; 5:3623-3648. [PMID: 35834795 DOI: 10.1021/acsabm.2c00415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deciphering the dynamics of intracellular organelles has gained immense attention due to their subtle control over diverse, complex biological processes such as cellular metabolism, energy homeostasis, and autophagy. In this context, molecular materials, including small-organic fluorescent probes and their supramolecular self-assembled nano-/microarchitectures, have been employed to explore the diverse intracellular biological events. However, only a handful of fluorescent probes and self-assembled emissive structures have been successfully used to track different organelle's movements, circumventing the issues related to water solubility and long-term photostability. Thus, the water-soluble molecular fluorescent probes and the water-dispersible supramolecular self-assemblies have emerged as promising candidates to explore the trafficking of the organelles under diverse physiological conditions. In this review, we have delineated the recent progress of fluorescent probes and their supramolecular self-assemblies for the elucidation of the dynamics of diverse cellular organelles with a special emphasis on lysosomes, lipid droplets, and mitochondria. Recent advancement in fluorescence lifetime and super-resolution microscopy imaging has also been discussed to investigate the dynamics of organelles. In addition, the fabrication of the next-generation molecular to supramolecular self-assembled luminogens for probing the variation of microenvironments during the trafficking process has been outlined.
Collapse
Affiliation(s)
- Subhankar Kundu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Subhadeep Das
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Shilpi Jaiswal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Abhijit Patra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| |
Collapse
|
23
|
Klier PEZ, Gest AMM, Martin JG, Roo R, Navarro MX, Lesiak L, Deal PE, Dadina N, Tyson J, Schepartz A, Miller EW. Bioorthogonal, Fluorogenic Targeting of Voltage-Sensitive Fluorophores for Visualizing Membrane Potential Dynamics in Cellular Organelles. J Am Chem Soc 2022; 144:12138-12146. [PMID: 35776693 DOI: 10.1021/jacs.2c02664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electrical potential differences across lipid bilayers play foundational roles in cellular physiology. Plasma membrane voltage is the most widely studied; however, the bilayers of organelles like mitochondria, lysosomes, nuclei, and the endoplasmic reticulum (ER) also provide opportunities for ionic compartmentalization and the generation of transmembrane potentials. Unlike plasma membranes, organellar bilayers, cloistered within the cell, remain recalcitrant to traditional approaches like patch-clamp electrophysiology. To address the challenge of monitoring changes in organelle membrane potential, we describe the design, synthesis, and application of the LUnAR RhoVR (Ligation Unquenched for Activation and Redistribution Rhodamine-based Voltage Reporter) for optically monitoring membrane potential changes in the ER of living cells. We pair a tetrazine-quenched RhoVR for voltage sensing with a transcyclooctene (TCO)-conjugated ceramide (Cer-TCO) for targeting to the ER. Bright fluorescence is observed only at the coincidence of the LUnAR RhoVR and TCO in the ER, minimizing non-specific, off-target fluorescence. We show that the product of the LUnAR RhoVR and Cer-TCO is voltage-sensitive and that the LUnAR RhoVR can be targeted to an intact ER in living cells. Using the LUnAR RhoVR, we use two-color, ER-localized, fast voltage imaging coupled with cytosolic Ca2+ imaging to validate the electroneutrality of Ca2+ release from internal stores. Finally, we use the LUnAR RhoVR to directly visualize functional coupling between the plasma-ER membranes in patch clamped cell lines, providing the first direct evidence of the sign of the ER potential response to plasma membrane potential changes. We envision that the LUnAR RhoVR, along with other existing organelle-targeting TCO probes, could be applied widely for exploring organelle physiology.
Collapse
Affiliation(s)
- Pavel E Z Klier
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Anneliese M M Gest
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Julia G Martin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ryan Roo
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Marisol X Navarro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Lauren Lesiak
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Parker E Deal
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Neville Dadina
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jonathan Tyson
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, United States
| |
Collapse
|
24
|
Heiss TK, Dorn RS, Ferreira AJ, Love AC, Prescher JA. Fluorogenic Cyclopropenones for Multicomponent, Real-Time Imaging. J Am Chem Soc 2022; 144:7871-7880. [PMID: 35442034 PMCID: PMC9377832 DOI: 10.1021/jacs.2c02058] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorogenic bioorthogonal reactions enable biomolecule visualization in real time. These reactions comprise reporters that "light up" upon reaction with complementary partners. While the spectrum of fluorogenic chemistries is expanding, few transformations are compatible with live cells due to cross-reactivities or insufficient signal turn-on. To address the need for more suitable chemistries for cellular imaging, we developed a fluorogenic reaction featuring cyclopropenone reporters and phosphines. The transformation involves regioselective activation and cyclization of cyclopropenones to form coumarin products. With optimal probes, the reaction provides >1600-fold signal turn-on, one of the highest fluorescence enhancements reported to date. The bioorthogonal motifs were evaluated in vitro and in cells. The reaction was also found to be compatible with other common fluorogenic transformations, enabling multicomponent, real-time imaging. Collectively, these data suggest that the cyclopropenone-phosphine reaction will bolster efforts to track biomolecule targets in their native settings.
Collapse
Affiliation(s)
- Tyler K Heiss
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Robert S Dorn
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Andrew J Ferreira
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Anna C Love
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| |
Collapse
|
25
|
Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
Collapse
Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
| |
Collapse
|
26
|
Geng Y, Zhang G, Chen Y, Peng Y, Wang X, Wang Z. Si-Rhodamine Derivatives for Brain Fluorescence Imaging and Monitoring of H2S in the Brain of Schizophrenic Mice before and after Treatment. Anal Chem 2022; 94:1813-1822. [DOI: 10.1021/acs.analchem.1c04611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yujie Geng
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guoyang Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuzhi Chen
- Institute of Health Service and Transfusion Medicine, Academy of Military Medical Sciences, Beijing 100039, P.R.China
| | - Yanghan Peng
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xuefei Wang
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
27
|
Wang N, Hao Y, Feng X, Zhu H, Zhang D, Wang T, Cui X. Silicon-substituted rhodamines for stimulated emission depletion fluorescence nanoscopy. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
28
|
Simon C, Feng S, Riezman H. Chemical Biology Tools to Study Lipids and their Metabolism with Increased Spatial and Temporal Resolution. Chimia (Aarau) 2021; 75:1012-1016. [PMID: 34920769 DOI: 10.2533/chimia.2021.1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lipids are important cellular components providing many essential functions. To fulfill these various functions evolution has selected for a diverse set of lipids and this diversity is seen at the organismal, cellular and subcellular level. Understanding how cells maintain this complex lipid organization is a very challenging problem, which for lipids, is not easily addressed using biochemical and genetic techniques. Therefore, chemical tools have an important role to play in our quest to understand the complexities of lipid metabolism. Here we discuss new chemical tools to study lipids, their distribution and metabolism with increased spatial and temporal resolution.
Collapse
Affiliation(s)
- Clémence Simon
- NCCR Chemical Biology, University of Geneva, CH-1211 Geneva
| | - Suihan Feng
- NCCR Chemical Biology, University of Geneva, CH-1211 Geneva; Current Address : Center for Microbes, Health and Development (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - Howard Riezman
- NCCR Chemical Biology, University of Geneva, CH-1211 Geneva;,
| |
Collapse
|
29
|
Jeong S, Widengren J, Lee JC. Fluorescent Probes for STED Optical Nanoscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 12:21. [PMID: 35009972 PMCID: PMC8746377 DOI: 10.3390/nano12010021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Progress in developing fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, is inseparable from the advancement in optical fluorescence microscopy. Super-resolution microscopy, or optical nanoscopy, overcame the far-field optical resolution limit, known as Abbe's diffraction limit, by taking advantage of the photophysical properties of fluorescent probes. Therefore, fluorescent probes for super-resolution microscopy should meet the new requirements in the probes' photophysical and photochemical properties. STED optical nanoscopy achieves super-resolution by depleting excited fluorophores at the periphery of an excitation laser beam using a depletion beam with a hollow core. An ideal fluorescent probe for STED nanoscopy must meet specific photophysical and photochemical properties, including high photostability, depletability at the depletion wavelength, low adverse excitability, and biocompatibility. This review introduces the requirements of fluorescent probes for STED nanoscopy and discusses the recent progress in the development of fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, for the STED nanoscopy. The strengths and the limitations of the fluorescent probes are analyzed in detail.
Collapse
Affiliation(s)
- Sejoo Jeong
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm 10691, Sweden;
| | - Jong-Chan Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
- New Biology Research Center, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea
| |
Collapse
|
30
|
Abstract
Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.
Collapse
Affiliation(s)
- Robert E Bird
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Steven A Lemmel
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Xiang Yu
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Qiongqiong Angela Zhou
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| |
Collapse
|
31
|
Zhao F, Wang W, Wu W. A novel ruthenium polypyridyl complex for the selective imaging and photodynamic targeting of the Golgi apparatus. Dalton Trans 2021; 50:3536-3541. [PMID: 33599670 DOI: 10.1039/d1dt00216c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A well-designed heteroleptic ruthenium(ii) polypyridyl complex demonstrated stable target-specific in vitro Golgi apparatus imaging abilities in HeLa cell lines. After utilizing photodynamic therapy via UV excitation, the Ru-SL complex could be triggered to generate singlet oxygen (1O2) and red fluorescence signals. 1O2 was highly cytotoxic and could induce DNA damage and the disappearance of the Golgi apparatus. The red fluorescence signals disappeared gradually, suggesting that the live or dead state of the cells can be estimated from the fluorescence signal intensity.
Collapse
Affiliation(s)
- Fengyi Zhao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China.
| | - Weifan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, China.
| |
Collapse
|
32
|
Synthetic probes and chemical tools in sphingolipid research. Curr Opin Chem Biol 2021; 65:126-135. [PMID: 34509716 DOI: 10.1016/j.cbpa.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022]
Abstract
Sphingolipids (SLs) are a unique class of nitrogen-linked lipids that are involved in membrane structure, cell signaling, and other important cellular processes. Abnormal sphingolipid metabolism is observed in several diseases including cancer, diabetes, metabolic disorders, and neurodegenerative diseases, such as Alzheimer's. However, the direct study of SLs has been hampered by their ubiquitous presence in cells and their complex metabolism. In the past few decades, efforts have been focused on creating synthetic probes and chemical tools to study SLs and decipher their roles in cellular biology. In this brief perspective, we seek to provide a concise snapshot of recently developed state-of-the-art chemical tools in SL research and the challenges that can be addressed through further development of SL probes.
Collapse
|
33
|
Broichhagen J, Kilian N. Chemical Biology Tools To Investigate Malaria Parasites. Chembiochem 2021; 22:2219-2236. [PMID: 33570245 PMCID: PMC8360121 DOI: 10.1002/cbic.202000882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Indexed: 02/06/2023]
Abstract
Parasitic diseases like malaria tropica have been shaping human evolution and history since the beginning of mankind. After infection, the response of the human host ranges from asymptomatic to severe and may culminate in death. Therefore, proper examination of the parasite's biology is pivotal to deciphering unique molecular, biochemical and cell biological processes, which in turn ensure the identification of treatment strategies, such as potent drug targets and vaccine candidates. However, implementing molecular biology methods for genetic manipulation proves to be difficult for many parasite model organisms. The development of fast and straightforward applicable alternatives, for instance small-molecule probes from the field of chemical biology, is essential. In this review, we will recapitulate the highlights of previous molecular and chemical biology approaches that have already created insight and understanding of the malaria parasite Plasmodium falciparum. We discuss current developments from the field of chemical biology and explore how their application could advance research into this parasite in the future. We anticipate that the described approaches will help to close knowledge gaps in the biology of P. falciparum and we hope that researchers will be inspired to use these methods to gain knowledge - with the aim of ending this devastating disease.
Collapse
Affiliation(s)
- Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Roessle-Strasse 1013125BerlinGermany
| | - Nicole Kilian
- Centre for Infectious DiseasesParasitologyHeidelberg University HospitalIm Neuenheimer Feld 32469120HeidelbergGermany
| |
Collapse
|
34
|
Wu Z, Xu X, Xi P. Stimulated emission depletion microscopy for biological imaging in four dimensions: A review. Microsc Res Tech 2021; 84:1947-1958. [PMID: 33713513 DOI: 10.1002/jemt.23750] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 02/27/2021] [Indexed: 12/26/2022]
Abstract
Stimulated emission depletion (STED) microscopy allows high lateral and axial resolution, long term imaging in living cells. Here we review recent technical advances in STED microscopy, with emphasis on resolution and measurement range of XYZt four dimensions. Different STED technical advances and novel STED probes are discussed with their respective application in biological subcellular imaging. This review may serve as a practical guide for choosing a suitable approach to the advanced STED super-resolution imaging.
Collapse
Affiliation(s)
- Zhaoyang Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Xinzhu Xu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Peng Xi
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.,UTS-SUSTech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| |
Collapse
|
35
|
Li W, Pan W, Huang M, Yang Z, He Y, Zhang W, Zhang J, Gu Z, Zhang D, Yan W, Qu J. Disulfide-Reduction-Triggered Spontaneous Photoblinking Cy5 Probe for Nanoscopic Imaging of Mitochondrial Dynamics in Live Cells. Anal Chem 2021; 93:2596-2602. [PMID: 33464055 DOI: 10.1021/acs.analchem.0c04658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria are highly dynamic organelles with interconnected tubule structures that are sensitive to environmental stress and light illumination. Super-resolution optical imaging of mitochondrial dynamics is of significance for understanding such biological events. Direct stochastic optical reconstruction microscopy has the advantages of a high spatial resolution, low phototoxicity in live-cell imaging, and the capacity to incorporate smart fluorescent probes. However, dSTORM imaging in live cells is challenging because of the requirement for an imaging buffer and a low temporal resolution. In this work, we achieved dSTORM imaging of mitochondrial dynamics in live cells with a disulfide-substituted Cy5 probe without using any toxic imaging buffer. Under the illumination of very low laser power, the probe exhibited spontaneous photoblinking triggered by disulfide-bond reduction in mitochondria of live cells. The obtained thiol attacked nearby carbon to form a six-membered ring and the reversible opening/closing of the ring produced spontaneous photoblinking behavior. With this new STORM strategy, we achieved observation of mitochondrial dynamics for more than 3 min, which provides a promising tool for further studies of mitochondria with an ultrafine structure.
Collapse
Affiliation(s)
- Wen Li
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenhui Pan
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Meina Huang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhigang Yang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ying He
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jianguo Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhenyu Gu
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Dan Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Yan
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Junle Qu
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
36
|
Chu L, Tyson J, Shaw JE, Rivera-Molina F, Koleske AJ, Schepartz A, Toomre DK. Two-color nanoscopy of organelles for extended times with HIDE probes. Nat Commun 2020; 11:4271. [PMID: 32848153 PMCID: PMC7450044 DOI: 10.1038/s41467-020-17859-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022] Open
Abstract
Performing multi-color nanoscopy for extended times is challenging due to the rapid photobleaching rate of most fluorophores. Here we describe a new fluorophore (Yale-595) and a bio-orthogonal labeling strategy that enables two-color super-resolution (STED) and 3D confocal imaging of two organelles simultaneously for extended times using high-density environmentally sensitive (HIDE) probes. Because HIDE probes are small, cell-permeant molecules, they can visualize dual organelle dynamics in hard-to-transfect cell lines by super-resolution for over an order of magnitude longer than with tagged proteins. The extended time domain possible using these tools reveals dynamic nanoscale targeting between different organelles. High density environmentally sensitive (HIDE) probes allow for long time-lapse super-resolution imaging of live cells. Here the authors develop a second HIDE probe with a bio-orthogonal labelling strategy to enable two-color nanoscopy of two organelles over extended periods.
Collapse
Affiliation(s)
- Ling Chu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Department of Chemistry, Yale University, New Haven, CT, USA
| | - Jonathan Tyson
- Department of Chemistry, Yale University, New Haven, CT, USA.,Department of Chemistry, University of California, Berkeley, CA, USA
| | - Juliana E Shaw
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Felix Rivera-Molina
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA. .,Department of Chemistry, University of California, Berkeley, CA, USA.
| | - Derek K Toomre
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
37
|
Flores J, White BM, Brea RJ, Baskin JM, Devaraj NK. Lipids: chemical tools for their synthesis, modification, and analysis. Chem Soc Rev 2020; 49:4602-4614. [PMID: 32691785 PMCID: PMC7380508 DOI: 10.1039/d0cs00154f] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipids remain one of the most enigmatic classes of biological molecules. Whereas lipids are well known to form basic units of membrane structure and energy storage, deciphering the exact roles and biological interactions of distinct lipid species has proven elusive. How these building blocks are synthesized, trafficked, and stored are also questions that require closer inspection. This tutorial review covers recent advances on the preparation, derivatization, and analysis of lipids. In particular, we describe several chemical approaches that form part of a powerful toolbox for controlling and characterizing lipid structure. We believe these tools will be helpful in numerous applications, including the study of lipid-protein interactions and the development of novel drug delivery systems.
Collapse
Affiliation(s)
- Judith Flores
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Brittany M White
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
38
|
Synthetic Sphingolipids with 1,2-Pyridazine Appendages Improve Antiproliferative Activity in Human Cancer Cell Lines. ACS Med Chem Lett 2020; 11:686-690. [PMID: 32435371 PMCID: PMC7236038 DOI: 10.1021/acsmedchemlett.9b00553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 12/22/2022] Open
Abstract
A synthetic sphingolipid related to a ring-constrained hydroxymethyl pyrrolidine analog of FTY720 that was known to starve cancer cells to death was chemically modified to include a series of alkoxy-tethered 3,6-substituted 1,2-pyridazines. These derivatives exhibited excellent antiproliferative activity against eight human cancer cell lines from four different cancer types. A 2.5- to 9-fold reduction in IC50 in these cell lines was observed relative to the lead compound, which lacked the appended heterocycle.
Collapse
|
39
|
Pigga JE, Fox JM. Flow Photochemical Syntheses of trans-Cyclooctenes and trans-Cycloheptenes Driven by Metal Complexation. Isr J Chem 2020; 60:207-218. [PMID: 34108738 PMCID: PMC8186252 DOI: 10.1002/ijch.201900085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Indexed: 12/19/2022]
Abstract
trans-Cyclooctenes and trans-cycloheptenes have long been the subject of physical organic study, but the broader application had been limited by synthetic accessibility. This account describes the development of a general, flow photochemical method for the preparative synthesis of trans-cycloalkene derivatives. Here, photoisom erization takes place in a closed-loop flow reactor where the reaction mixture is continuously cycled through Ag(I) on silica gel. Selective complexation of the trans-isomer by Ag(I) during flow drives an otherwise unfavorable isomeric ratio toward the trans-isomer. Analogous photoreactions under batch-conditions are low yielding, and flow chemistry is necessary in order to obtain trans-cycloalkenes in preparatively useful yields. The applications of the method to bioorthogonal chemistry and stereospecific transannulation chemistry are described.
Collapse
Affiliation(s)
- Jessica E Pigga
- Department of Chemistry and Biochemistry University of Delaware, Newark DE 19716
| | - Joseph M Fox
- Department of Chemistry and Biochemistry University of Delaware, Newark DE 19716
| |
Collapse
|
40
|
Gupta A, Rivera-Molina F, Xi Z, Toomre D, Schepartz A. Endosome motility defects revealed at super-resolution in live cells using HIDE probes. Nat Chem Biol 2020; 16:408-414. [PMID: 32094922 PMCID: PMC7176048 DOI: 10.1038/s41589-020-0479-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022]
Abstract
We report new lipid-based, high-density, environmentally sensitive (HIDE) probes that accurately and selectively image endo-lysosomes and their dynamics at super-resolution for extended times. Treatment of live cells with the small molecules DiIC16TCO or DiIC16’TCO followed by in situ tetrazine ligation reaction with the silicon-rhodamine dye SiR-Tz generates the HIDE probes DiIC16-SiR and DiIC16’-SiR in the endo-lysosomal membrane. These new probes support the acquisition of super-resolution videos of organelle dynamics in primary cells for more than 7 minutes with no detectable change in endosome structure or function. Using DiIC16-SiR and DiIC16’-SiR, we describe the first direct evidence of endosome motility defects in cells from patients with Niemann-Pick Type-C disease. In wild-type fibroblasts, the probes reveal distinct but rare inter-endosome kiss-and-run events that cannot be observed using confocal methods. Our results shed new light on the role of NPC1 in organelle motility and cholesterol trafficking.
Collapse
Affiliation(s)
- Aarushi Gupta
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Felix Rivera-Molina
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zhiqun Xi
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA. .,Department of Chemistry, University of California, Berkeley, CA, USA.
| |
Collapse
|
41
|
Liang L, Yan W, Qin X, Peng X, Feng H, Wang Y, Zhu Z, Liu L, Han Y, Xu Q, Qu J, Liu X. Designing Sub‐2 nm Organosilica Nanohybrids for Far‐Field Super‐Resolution Imaging. Angew Chem Int Ed Engl 2020; 59:746-751. [DOI: 10.1002/anie.201912404] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Liangliang Liang
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Wei Yan
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Xian Qin
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Han Feng
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research InstituteInterdisciplinary Graduate ProgrammeNanyang Technological University Singapore 637141 Singapore
| | - Yu Wang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & TechnologyInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationInstitute of Microscale OptoelectronicsShenzhen University Shenzhen 518060 China
- Engineering Technology Research Center for 2D Material Information Function Devices and Systems of Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Ziyu Zhu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Lingmei Liu
- King Abdullah University of Science and TechnologyPhysical Sciences and Engineering DivisionAdvanced Membranes and Porous Materials Center Thuwal Saudi Arabia
| | - Yu Han
- King Abdullah University of Science and TechnologyPhysical Sciences and Engineering DivisionAdvanced Membranes and Porous Materials Center Thuwal Saudi Arabia
| | - Qinghua Xu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Xiaogang Liu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & TechnologyInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationInstitute of Microscale OptoelectronicsShenzhen University Shenzhen 518060 China
| |
Collapse
|
42
|
Zhao M, Guo YS, Xu WN, Zhao YF, Xie HY, Li HJ, Chen XF, Zhao RS, Guo DS. Far-red to near-infrared fluorescent probes based on silicon-substituted xanthene dyes for sensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115704] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
43
|
Liang L, Yan W, Qin X, Peng X, Feng H, Wang Y, Zhu Z, Liu L, Han Y, Xu Q, Qu J, Liu X. Designing Sub‐2 nm Organosilica Nanohybrids for Far‐Field Super‐Resolution Imaging. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Liangliang Liang
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Wei Yan
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Xian Qin
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Han Feng
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research InstituteInterdisciplinary Graduate ProgrammeNanyang Technological University Singapore 637141 Singapore
| | - Yu Wang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & TechnologyInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationInstitute of Microscale OptoelectronicsShenzhen University Shenzhen 518060 China
- Engineering Technology Research Center for 2D Material Information Function Devices and Systems of Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Ziyu Zhu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Lingmei Liu
- King Abdullah University of Science and TechnologyPhysical Sciences and Engineering DivisionAdvanced Membranes and Porous Materials Center Thuwal Saudi Arabia
| | - Yu Han
- King Abdullah University of Science and TechnologyPhysical Sciences and Engineering DivisionAdvanced Membranes and Porous Materials Center Thuwal Saudi Arabia
| | - Qinghua Xu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen University Shenzhen 518060 China
| | - Xiaogang Liu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & TechnologyInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationInstitute of Microscale OptoelectronicsShenzhen University Shenzhen 518060 China
| |
Collapse
|
44
|
Li M, Li Y, Wang X, Cui X, Wang T. Synthesis and application of near-infrared substituted rhodamines. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
45
|
Matthias J, Kanagasundaram T, Kopka K, Kramer CS. Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement. Beilstein J Org Chem 2019; 15:2333-2343. [PMID: 31666868 PMCID: PMC6808212 DOI: 10.3762/bjoc.15.226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Since their first synthesis, silicon xanthenes and the subsequently developed silicon rhodamines (SiR) gained a lot of attention as attractive fluorescence dyes offering a broad field of application. We aimed for the synthesis of a fluorinable pyridinyl silicon rhodamine for the use in multimodal (PET/OI) medical imaging of mitochondria in cancerous cells. Results: A dihalogenated fluorinatable pyridinyl rhodamine could be successfully synthesized with the high yield of 85% by application of a halogen dance (HD) rearrangement. The near-infrared dye shows a quantum yield of 0.34, comparable to other organelle targeting SiR derivatives and absorbs at 665 nm (εmax = 34 000 M−1cm−1) and emits at 681 nm (τ = 1.9 ns). Using colocalization experiments with MitoTracker® Green FM, we could prove the intrinsic targeting ability to mitochondria in two human cell lines (Pearson coefficient >0.8). The dye is suitable for live cell STED nanoscopy imaging and shows a nontoxic profile which makes it an appropriate candidate for medical imaging. Conclusions: We present a biocompatible, nontoxic, small molecule near-infrared dye with the option of subsequent radiolabelling and excellent optical properties for medical and bioimaging. As a compound with intrinsic mitochondria targeting ability, the radiolabelled analogue can be applied in multimodal (PET/OI) imaging of mitochondria for diagnostic and therapeutic use in, e.g., cancer patients.
Collapse
Affiliation(s)
- Jessica Matthias
- Max Planck Institute for Medical Research, Department of Optical Nanoscopy, Jahnstraße 29, 69120 Heidelberg, Germany.,Helmholtz International Graduate School, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany
| | - Thines Kanagasundaram
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany.,Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Klaus Kopka
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carsten S Kramer
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 223, 69120 Heidelberg, Germany
| |
Collapse
|
46
|
Hua XW, Bao YW, Zeng J, Wu FG. Nucleolus-Targeted Red Emissive Carbon Dots with Polarity-Sensitive and Excitation-Independent Fluorescence Emission: High-Resolution Cell Imaging and in Vivo Tracking. ACS APPLIED MATERIALS & INTERFACES 2019; 11:32647-32658. [PMID: 31381288 DOI: 10.1021/acsami.9b09590] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Red-emitting carbon dots (CDs) have attracted tremendous attention due to their wide applications in areas including imaging, sensing, drug delivery, and cancer therapy. However, it is still highly challenging for red-emitting CDs to simultaneously achieve high quantum yields (QYs), nucleus targeting, and super-resolution fluorescence imaging (especially the stimulated emission depletion (STED) imaging). Here, it is found that the addition of varied metal ions during the hydrothermal treatment of p-phenylenediamine (pPDA) leads to the formation of fluorescent CDs with emission wavelengths up to 700 nm. Strikingly, although metal ions play a crucial role in the synthesis of CDs with varied QYs, they are absent in the formed CDs, that is, the obtained CDs are metal-free, and the metal ions play a role similar to a "catalyst" during the CD formation. Besides, using pPDA and nickel ions (Ni2+) as raw materials, we prepare Ni-pPCDs which have the highest QY and exhibit various excellent fluorescence properties including excitation-independent emission (at ∼605 nm), good photostability, polarity sensitivity, and ribonucleic acid responsiveness. In vitro and in vivo experiments demonstrate that Ni-pPCDs are highly biocompatible and can realize real-time, wash-free, and high-resolution imaging of cell nuclei and high-contrast imaging of tumor-bearing mice and zebrafish. In summary, the present work may hold great promise in the synthesis and applications of red emissive CDs.
Collapse
|
47
|
A real-time, click chemistry imaging approach reveals stimulus-specific subcellular locations of phospholipase D activity. Proc Natl Acad Sci U S A 2019; 116:15453-15462. [PMID: 31311871 DOI: 10.1073/pnas.1903949116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fidelity of signal transduction requires spatiotemporal control of the production of signaling agents. Phosphatidic acid (PA) is a pleiotropic lipid second messenger whose modes of action differ based on upstream stimulus, biosynthetic source, and site of production. How cells regulate the local production of PA to effect diverse signaling outcomes remains elusive. Unlike other second messengers, sites of PA biosynthesis cannot be accurately visualized with subcellular precision. Here, we describe a rapid, chemoenzymatic approach for imaging physiological PA production by phospholipase D (PLD) enzymes. Our method capitalizes on the remarkable discovery that bulky, hydrophilic trans-cyclooctene-containing primary alcohols can supplant water as the nucleophile in the PLD active site in a transphosphatidylation reaction of PLD's lipid substrate, phosphatidylcholine. The resultant trans-cyclooctene-containing lipids are tagged with a fluorogenic tetrazine reagent via a no-rinse, inverse electron-demand Diels-Alder (IEDDA) reaction, enabling their immediate visualization by confocal microscopy in real time. Strikingly, the fluorescent reporter lipids initially produced at the plasma membrane (PM) induced by phorbol ester stimulation of PLD were rapidly internalized via apparent nonvesicular pathways rather than endocytosis, suggesting applications of this activity-based imaging toolset for probing mechanisms of intracellular phospholipid transport. By instead focusing on the initial 10 s of the IEDDA reaction, we precisely pinpointed the subcellular locations of endogenous PLD activity as elicited by physiological agonists of G protein-coupled receptor and receptor tyrosine kinase signaling. These tools hold promise to shed light on both lipid trafficking pathways and physiological and pathological effects of localized PLD signaling.
Collapse
|
48
|
Wu H, Devaraj NK. Mining Proteomes Using Bioorthogonal Probes. Cell Chem Biol 2019; 23:751-753. [PMID: 27447043 DOI: 10.1016/j.chembiol.2016.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The definition of proteomes in cells and animals at particular stages facilitates an understanding of protein function. In this issue of Cell Chemical Biology, Elliott et al. (2016) report an elegant approach of bioorthogonal labeling and enrichment of proteomes from stochastic orthogonal recoding of translation. With this method, low abundance proteomes can be identified in a multicellular system.
Collapse
Affiliation(s)
- Haoxing Wu
- Department of Radiology, Huaxi MR Research Center (HMRRC), West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
49
|
Collenburg L, Schneider-Schaulies S, Avota E. The neutral sphingomyelinase 2 in T cell receptor signaling and polarity. Biol Chem 2019; 399:1147-1155. [PMID: 29337691 DOI: 10.1515/hsz-2017-0280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/31/2017] [Indexed: 01/13/2023]
Abstract
By hydrolyzing its substrate sphingomyelin at the cytosolic leaflet of cellular membranes, the neutral sphingomyelinase 2 (NSM2) generates microdomains which serve as docking sites for signaling proteins and thereby, functions to regulate signal relay. This has been particularly studied in cellular stress responses while the regulatory role of this enzyme in the immune cell compartment has only recently emerged. In T cells, phenotypic polarization by co-ordinated cytoskeletal remodeling is central to motility and interaction with endothelial or antigen-presenting cells during tissue recruitment or immune synapse formation, respectively. This review highlights studies adressing the role of NSM2 in T cell polarity in which the enzyme plays a major role in regulating cytoskeletal dynamics.
Collapse
Affiliation(s)
- Lena Collenburg
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, D-97078 Würzburg, Germany
| | - Sibylle Schneider-Schaulies
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, D-97078 Würzburg, Germany
| | - Elita Avota
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, D-97078 Würzburg, Germany
| |
Collapse
|
50
|
Fink J, Seibel J. Click reactions with functional sphingolipids. Biol Chem 2019; 399:1157-1168. [PMID: 29908120 DOI: 10.1515/hsz-2018-0169] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/15/2018] [Indexed: 12/17/2022]
Abstract
Sphingolipids and glycosphingolipids can regulate cell recognition and signalling. Ceramide and sphingosine-1-phosphate are major players in the sphingolipid pathways and are involved in the initiation and regulation of signalling, apoptosis, stress responses and infection. Specific chemically synthesised sphingolipid derivatives containing small functionalities like azide or alkyne can mimic the biological properties of natural lipid species, which turns them into useful tools for the investigation of the highly complex sphingolipid metabolism by rapid and selective 'click chemistry' using sensitive tags like fluorophores. Subsequent analysis by various fluorescence microscopy techniques or mass spectrometry allows the identification and quantification of the corresponding sphingolipid metabolites as well as the research of associated enzymes. Here we present an overview of recent advances in the synthesis of ceramide and sphingosine analogues for bioorthogonal click reactions to study biosynthetic pathways and localization of sphingolipids for the development of novel therapeutics against lipid-dependent diseases.
Collapse
Affiliation(s)
- Julian Fink
- University of Würzburg, Institute of Organic Chemistry, Am Hubland, D-97074 Würzburg, Germany
| | - Jürgen Seibel
- University of Würzburg, Institute of Organic Chemistry, Am Hubland, D-97074 Würzburg, Germany
| |
Collapse
|