1
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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.
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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.
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2
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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.
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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.
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3
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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.
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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
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4
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Martins TS, Costa RS, Vilaça R, Lemos C, Teixeira V, Pereira C, Costa V. Iron Limitation Restores Autophagy and Increases Lifespan in the Yeast Model of Niemann–Pick Type C1. Int J Mol Sci 2023; 24:ijms24076221. [PMID: 37047194 PMCID: PMC10094029 DOI: 10.3390/ijms24076221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Niemann–Pick type C1 (NPC1) is an endolysosomal transmembrane protein involved in the export of cholesterol and sphingolipids to other cellular compartments such as the endoplasmic reticulum and plasma membrane. NPC1 loss of function is the major cause of NPC disease, a rare lysosomal storage disorder characterized by an abnormal accumulation of lipids in the late endosomal/lysosomal network, mitochondrial dysfunction, and impaired autophagy. NPC phenotypes are conserved in yeast lacking Ncr1, an orthologue of human NPC1, leading to premature aging. Herein, we performed a phosphoproteomic analysis to investigate the effect of Ncr1 loss on cellular functions mediated by the yeast lysosome-like vacuoles. Our results revealed changes in vacuolar membrane proteins that are associated mostly with vesicle biology (fusion, transport, organization), autophagy, and ion homeostasis, including iron, manganese, and calcium. Consistently, the cytoplasm to vacuole targeting (Cvt) pathway was increased in ncr1∆ cells and autophagy was compromised despite TORC1 inhibition. Moreover, ncr1∆ cells exhibited iron overload mediated by the low-iron sensing transcription factor Aft1. Iron deprivation restored the autophagic flux of ncr1∆ cells and increased its chronological lifespan and oxidative stress resistance. These results implicate iron overload on autophagy impairment, oxidative stress sensitivity, and cell death in the yeast model of NPC1.
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5
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Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
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6
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Abstract
Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an all-small molecule approach that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy (LExM), to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. Compatible with standard confocal microscopes, LExM will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts.
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Affiliation(s)
- Brittany M White
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Pratik Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, United States
| | - Amanda N Conwell
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kane Wu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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7
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Tamura T, Hamachi I. Chemical biology tools for imaging-based analysis of organelle membranes and lipids. Curr Opin Chem Biol 2022; 70:102182. [PMID: 35779350 DOI: 10.1016/j.cbpa.2022.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
Membrane biology studies have revealed that in addition to providing structural support for compartment formation and membrane protein function, subcellular biomembranes are also critically involved in many biological events. To facilitate our understanding of the functions, biophysical properties and structural dynamics of organelle membranes, various exciting chemical biology tools have recently emerged. This short review aims to describe the latest molecular probes for organelle membrane studies. In particular, we will feature chemical strategies to visualize and quantitatively analyze the dynamic propeties of organelle membranes and lipids and discuss current limitations and potential future directions of this challenging research area.
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Affiliation(s)
- Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan; ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan.
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8
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Levine PM, Craven TW, Li X, Balana AT, Bird GH, Godes M, Salveson PJ, Erickson PW, Lamb M, Ahlrichs M, Murphy M, Ogohara C, Said MY, Walensky LD, Pratt MR, Baker D. Generation of Potent and Stable GLP-1 Analogues Via "Serine Ligation". ACS Chem Biol 2022; 17:804-809. [PMID: 35319882 PMCID: PMC9173702 DOI: 10.1021/acschembio.2c00075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide and protein bioconjugation technologies have revolutionized our ability to site-specifically or chemoselectively install a variety of functional groups for applications in chemical biology and medicine, including the enhancement of bioavailability. Here, we introduce a site-specific bioconjugation strategy inspired by chemical ligation at serine that relies on a noncanonical amino acid containing a 1-amino-2-hydroxy functional group and a salicylaldehyde ester. More specifically, we harness this technology to generate analogues of glucagon-like peptide-1 that resemble Semaglutide, a long-lasting blockbuster drug currently used in the clinic to regulate glucose levels in the blood. We identify peptides that are more potent than unmodified peptide and equipotent to Semaglutide in a cell-based activation assay, improve the stability in human serum, and increase glucose disposal efficiency in vivo. This approach demonstrates the potential of "serine ligation" for various applications in chemical biology, with a particular focus on generating stabilized peptide therapeutics.
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Affiliation(s)
- Paul M. Levine
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Timothy W. Craven
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Xinting Li
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | | | | | | | - Patrick J. Salveson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Patrick W. Erickson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Mila Lamb
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Maggie Ahlrichs
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Michael Murphy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Cassandra Ogohara
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Meerit Y. Said
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | | | | | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
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9
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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]
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10
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Dadina N, Tyson J, Zheng S, Lesiak L, Schepartz A. Imaging organelle membranes in live cells at the nanoscale with lipid-based fluorescent probes. Curr Opin Chem Biol 2021; 65:154-162. [PMID: 34715587 PMCID: PMC9904808 DOI: 10.1016/j.cbpa.2021.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022]
Abstract
Understanding how organelles interact, exchange materials, assemble, disassemble, and evolve as a function of space, time, and environment is an exciting area at the very forefront of chemical and cell biology. Here, we bring attention to recent progress in the design and application of lipid-based tools to visualize and interrogate organelles in live cells, especially at super resolution. We highlight strategies that rely on modification of natural lipids or lipid-like small molecules ex cellula, where organelle specificity is provided by the structure of the chemically modified lipid, or in cellula using cellular machinery, where an enzyme labels the lipid in situ. We also describe recent improvements to the chemistry upon which lipid probes rely, many of which have already begun to broaden the scope of biological questions that can be addressed by imaging organelle membranes at the nanoscale.
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Affiliation(s)
- N. Dadina
- Department of Chemistry, University of California, Berkeley 94720, USA
| | - J. Tyson
- Department of Chemistry, University of California, Berkeley 94720, USA
| | - S. Zheng
- Department of Chemistry, University of California, Berkeley 94720, USA
| | - L. Lesiak
- Department of Chemistry, University of California, Berkeley 94720, USA
| | - A. Schepartz
- Department of Chemistry, University of California, Berkeley 94720, USA,Department of Molecular & Cell Biology, University of California, Berkeley 94720, USA,California Institute for Quantitative Biosciences, University of California, Berkeley 94720, USA
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11
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Abstract
Fluorescent tools have emerged as an important tool for studying the distinct chemical microenvironments of organelles, due to their high specificity and ability to be used in non-destructive, live cellular studies. These tools fall largely in two categories: exogenous fluorescent dyes, or endogenous labels such as genetically encoded fluorescent proteins. In both cases, the probe must be targeted to the organelle of interest. To date, many organelle-targeted fluorescent tools have been reported and used to uncover new information about processes that underpin health and disease. However, the majority of these tools only apply a handful of targeting groups, and less-studied organelles have few robust targeting strategies. While the development of new, robust strategies is difficult, it is essential to develop such strategies to allow for the development of new tools and broadening the effective study of organelles. This review aims to provide a comprehensive overview of the major targeting strategies for both endogenous and exogenous fluorescent cargo, outlining the specific challenges for targeting each organelle type and as well as new developments in the field.
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Affiliation(s)
- Jiarun Lin
- School of Chemistry, The University of Sydney, NSW, 2006, Australia.
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, NSW 2006, Australia
| | - Kylie Yang
- School of Chemistry, The University of Sydney, NSW, 2006, Australia.
| | - Elizabeth J New
- School of Chemistry, The University of Sydney, NSW, 2006, Australia.
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW 2006, Australia
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12
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Fan M, An H, Wang C, Huo S, Wang T, Cui X, Zhang D. STED Imaging the Dynamics of Lysosomes by Dually Fluorogenic Si-Rhodamine. Chemistry 2021; 27:9620-9626. [PMID: 33899976 DOI: 10.1002/chem.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Indexed: 11/07/2022]
Abstract
Super-resolution microscopy (SRM) imaging of the finite subcellular structures and subtle bioactivities inside organelles delivers abundant cellular information with high fidelity to unravel the intricate biological processes. An ideal fluorescent probe with precise control of fluorescence is critical in SRM technique like stimulated emission depletion (STED). Si-rhodamine was decorated with both targeting group and H+ -receptor, affording the dually fluorogenic Si-rhodamine in which the NIR fluorescence was efficiently controlled by the coalescent of spirolactone-zwitterion equilibrium and PeT mechanism. The dually fluorogenic characters of the probe offer a perfect mutual enhancement in sensitivity, specificity and spatial resolution. Strong fluorescence only released in the existence of targeting protein at acidic lysosomal pH, ensured precisely tracking the dynamic of lysosomal structure and pH in living cells by STED.
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Affiliation(s)
- Mengting Fan
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Haiyan An
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
| | - Chuanfeng Wang
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Shuhui Huo
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Ting Wang
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
| | - Xiaoyan Cui
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Dazhi Zhang
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
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13
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Sheridan E, Vercellino S, Cursi L, Adumeau L, Behan JA, Dawson KA. Understanding intracellular nanoparticle trafficking fates through spatiotemporally resolved magnetic nanoparticle recovery. NANOSCALE ADVANCES 2021; 3:2397-2410. [PMID: 36134166 PMCID: PMC9419038 DOI: 10.1039/d0na01035a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/21/2021] [Indexed: 05/08/2023]
Abstract
The field of nanomedicine has the potential to be a game-changer in global health, with possible applications in prevention, diagnostics, and therapeutics. However, despite extensive research focus and funding, the forecasted explosion of novel nanomedicines is yet to materialize. We believe that clinical translation is ultimately hampered by a lack of understanding of how nanoparticles really interact with biological systems. When placed in a biological environment, nanoparticles adsorb a biomolecular layer that defines their biological identity. The challenge for bionanoscience is therefore to understand the evolution of the interactions of the nanoparticle-biomolecules complex as the nanoparticle is trafficked through the intracellular environment. However, to progress on this route, scientists face major challenges associated with isolation of specific intracellular compartments for analysis, complicated by the diversity of trafficking events happening simultaneously and the lack of synchronization between individual events. In this perspective article, we reflect on how magnetic nanoparticles can help to tackle some of these challenges as part of an overall workflow and act as a useful platform to investigate the bionano interactions within the cell that contribute to this nanoscale decision making. We discuss both established and emerging techniques for the magnetic extraction of nanoparticles and how they can potentially be used as tools to study the intracellular journey of nanomaterials inside the cell, and their potential to probe nanoscale decision-making events. We outline the inherent limitations of these techniques when investigating particular bio-nano interactions along with proposed strategies to improve both specificity and resolution. We conclude by describing how the integration of magnetic nanoparticle recovery with sophisticated analysis at the single-particle level could be applied to resolve key questions for this field in the future.
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Affiliation(s)
- Emily Sheridan
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - Silvia Vercellino
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Biomolecular and Biomedical Science, University College Dublin Belfield Dublin 4 Ireland
| | - Lorenzo Cursi
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - Laurent Adumeau
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - James A Behan
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - Kenneth A Dawson
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
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14
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Work EM, Ferraudi G, Kiefer L, Liu G, Grigalunas M, Bhardwaj A, Kaur R, Dempsey JM, Wüstner D, Helquist P, Wiest O. Design, Synthesis, and Evaluation of a Luminescent Cholesterol Mimic. J Org Chem 2021; 86:1612-1621. [PMID: 33369429 PMCID: PMC8126345 DOI: 10.1021/acs.joc.0c02460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of new chemical tools with improved properties is essential to chemical and cell biology. Of particular interest is the development of mimics of small molecules with important cellular function that allow the direct observation of their trafficking in a cell. To this end, a novel 15-azasterol has been designed and synthesized as a luminescent cholesterol mimic for the monitoring of cholesterol trafficking. The brightness of this probe, which is ∼32-times greater than the widely used dehydroergosterol probe, is combined with resistance to photobleaching in solution and in human fibroblasts and an exceptionally large Stokes-like shift of ∼150-200 nm. The photophysical properties of the probe have been studied experimentally and computationally, suggesting an intersystem crossing to the triplet excited state with subsequent phosphorescent decay. Molecular dynamics simulations show a similar binding mode of cholesterol and the azasterol probe to NPC proteins, demonstrating the structural similarity of the probe to cholesterol.
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Affiliation(s)
- Emily M. Work
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Guillermo Ferraudi
- Radiation Research Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Luke Kiefer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Gang Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Michael Grigalunas
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Atul Bhardwaj
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Rasmin Kaur
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Janel M. Dempsey
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46566, United States
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15
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Tamura T, Fujisawa A, Tsuchiya M, Shen Y, Nagao K, Kawano S, Tamura Y, Endo T, Umeda M, Hamachi I. Organelle membrane-specific chemical labeling and dynamic imaging in living cells. Nat Chem Biol 2020; 16:1361-1367. [PMID: 32958953 DOI: 10.1038/s41589-020-00651-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/14/2020] [Indexed: 12/22/2022]
Abstract
Lipids play crucial roles as structural elements, signaling molecules and material transporters in cells. However, the functions and dynamics of lipids within cells remain unclear because of a lack of methods to selectively label lipids in specific organelles and trace their movement by live-cell imaging. We describe here a technology for the selective labeling and fluorescence imaging (microscopic or nanoscopic) of phosphatidylcholine in target organelles. This approach involves the metabolic incorporation of azido-choline, followed by a spatially limited bioorthogonal reaction that enables the visualization and quantitative analysis of interorganelle lipid transport in live cells. More importantly, with live-cell imaging, we obtained direct evidence that the autophagosomal membrane originates from the endoplasmic reticulum. This method is simple and robust and is thus powerful for real-time tracing of interorganelle lipid trafficking.
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Affiliation(s)
- Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Alma Fujisawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Masaki Tsuchiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Yuying Shen
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kohjiro Nagao
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shin Kawano
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, Yamagata, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Masato Umeda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan.
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16
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Krishnan Y, Zou J, Jani MS. Quantitative Imaging of Biochemistry in Situ and at the Nanoscale. ACS CENTRAL SCIENCE 2020; 6:1938-1954. [PMID: 33274271 PMCID: PMC7706076 DOI: 10.1021/acscentsci.0c01076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Indexed: 05/12/2023]
Abstract
Biochemical reactions in eukaryotic cells occur in subcellular, membrane-bound compartments called organelles. Each kind of organelle is characterized by a unique lumenal chemical composition whose stringent regulation is vital to proper organelle function. Disruption of the lumenal ionic content of organelles is inextricably linked to disease. Despite their vital roles in cellular homeostasis, there are large gaps in our knowledge of organellar chemical composition largely from a lack of suitable probes. In this Outlook, we describe how, using organelle-targeted ratiometric probes, one can quantitatively image the lumenal chemical composition and biochemical activity inside organelles. We discuss how excellent fluorescent detection chemistries applied largely to the cytosol may be expanded to study organelles by chemical imaging at subcellular resolution in live cells. DNA-based reporters are a new and versatile platform to enable such approaches because the resultant probes have precise ratiometry and accurate subcellular targeting and are able to map multiple chemicals simultaneously. Quantitatively mapping lumenal ions and biochemical activity can drive the discovery of new biology and biomedical applications.
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Affiliation(s)
| | - Junyi Zou
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Grossman Institute of Neuroscience,
Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637, United States
| | - Maulik S. Jani
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Grossman Institute of Neuroscience,
Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637, United States
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