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Goldman C, Kareva T, Sarrafha L, Schuldt BR, Sahasrabudhe A, Ahfeldt T, Blanchard JW. Genetically Encoded and Modular SubCellular Organelle Probes (GEM-SCOPe) reveal lysosomal and mitochondrial dysfunction driven by PRKN knockout. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.594886. [PMID: 38979135 PMCID: PMC11230217 DOI: 10.1101/2024.05.21.594886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cellular processes including lysosomal and mitochondrial dysfunction are implicated in the development of many diseases. Quantitative visualization of mitochondria and lysosoesl is crucial to understand how these organelles are dysregulated during disease. To address a gap in live-imaging tools, we developed GEM-SCOPe (Genetically Encoded and Modular SubCellular Organelle Probes), a modular toolbox of fluorescent markers designed to inform on localization, distribution, turnover, and oxidative stress of specific organelles. We expressed GEM-SCOPe in differentiated astrocytes and neurons from a human pluripotent stem cell PRKN-knockout model of Parkinson's disease and identified disease-associated changes in proliferation, lysosomal distribution, mitochondrial transport and turnover, and reactive oxygen species. We demonstrate GEM-SCOPe is a powerful panel that provide critical insight into the subcellular mechanisms underlying Parkinson's disease in human cells. GEM-SCOPe can be expanded upon and applied to a diversity of cellular models to glean an understanding of the mechanisms that promote disease onset and progression.
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Affiliation(s)
- Camille Goldman
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Tatyana Kareva
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Braxton R. Schuldt
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Abhishek Sahasrabudhe
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Joel W. Blanchard
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
- Lead Contact
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Yan Y, Xiao J, Huang F, Xian W, Yu B, Cheng R, Wu H, Lu X, Wang X, Huang W, Li J, Oyejobi GK, Robinson CV, Wu H, Wu D, Liu X, Wang L, Zhu B. Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway. Nat Microbiol 2024; 9:1566-1578. [PMID: 38649411 DOI: 10.1038/s41564-024-01684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
The cyclic-oligonucleotide-based anti-phage signalling system (CBASS) is a type of innate prokaryotic immune system. Composed of a cyclic GMP-AMP synthase (cGAS) and CBASS-associated proteins, CBASS uses cyclic oligonucleotides to activate antiviral immunity. One major class of CBASS contains a homologue of eukaryotic ubiquitin-conjugating enzymes, which is either an E1-E2 fusion or a single E2. However, the functions of single E2s in CBASS remain elusive. Here, using biochemical, genetic, cryo-electron microscopy and mass spectrometry investigations, we discover that the E2 enzyme from Serratia marcescens regulates cGAS by imitating the ubiquitination cascade. This includes the processing of the cGAS C terminus, conjugation of cGAS to a cysteine residue, ligation of cGAS to a lysine residue, cleavage of the isopeptide bond and poly-cGASylation. The poly-cGASylation activates cGAS to produce cGAMP, which acts as an antiviral signal and leads to cell death. Thus, our findings reveal a unique regulatory role of E2 in CBASS.
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Affiliation(s)
- Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Xiao
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.
| | - Wei Xian
- Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjing Huang
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jing Li
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Greater Kayode Oyejobi
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Xiaoyun Liu
- Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
| | - Longfei Wang
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.
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3
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Aeindartehran L, Sadri Z, Rahimi F, Alinejad T. Fluorescence in depth: integration of spectroscopy and imaging with Raman, IR, and CD for advanced research. Methods Appl Fluoresc 2024; 12:032002. [PMID: 38697201 DOI: 10.1088/2050-6120/ad46e6] [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: 12/27/2023] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
Fluorescence spectroscopy serves as a vital technique for studying the interaction between light and fluorescent molecules. It encompasses a range of methods, each presenting unique advantages and applications. This technique finds utility in various chemical studies. This review discusses Fluorescence spectroscopy, its branches such as Time-Resolved Fluorescence Spectroscopy (TRFS) and Fluorescence Lifetime Imaging Microscopy (FLIM), and their integration with other spectroscopic methods, including Raman, Infrared (IR), and Circular Dichroism (CD) spectroscopies. By delving into these methods, we aim to provide a comprehensive understanding of the capabilities and significance of fluorescence spectroscopy in scientific research, highlighting its diverse applications and the enhanced understanding it brings when combined with other spectroscopic methods. This review looks at each technique's unique features and applications. It discusses the prospects of their combined use in advancing scientific understanding and applications across various domains.
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Affiliation(s)
- Lida Aeindartehran
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Zahra Sadri
- Department of Biological Science, Southern Methodist University, Dallas, Texas 75205, United States of America
| | - Fateme Rahimi
- Department of Chemical Engineering, Babol Noshirvani University of Technology, Babol, Iran
| | - Tahereh Alinejad
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou 325015, Zhejiang, People's Republic of China
- Institute of Cell Growth Factor, Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision, and Brain Health), Wenzhou Medical University, Wenzhou 325000, People's Republic of China
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Ghaffari Zaki A, Yiğit EN, Aydın MŞ, Vatandaslar E, Öztürk G, Eroglu E. Genetically Encoded Biosensors Unveil Neuronal Injury Dynamics via Multichromatic ATP and Calcium Imaging. ACS Sens 2024; 9:1261-1271. [PMID: 38293866 DOI: 10.1021/acssensors.3c02111] [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] [Indexed: 02/01/2024]
Abstract
When a cell sustains damage, it liberates cytosolic ATP, which can serve as an injury signal, affecting neighboring cells. This study presents a methodological approach that employs in vitro axotomy and in vivo laser ablation to simulate cellular injury. Specially tailored biosensors are employed to monitor ATP dynamics and calcium transients in injured cells and their surroundings. To simultaneously visualize extracellular and cytosolic ATP, we developed bicistronic constructs featuring GRABATP1.0 and MaLionR biosensors alongside the calcium sensor RCaMP, enabling multiparametric imaging. In addition to transducing primary neuron cultures, we developed another method where we cocultured dorsal root ganglion neurons together with specialized "sniffer" cell lines expressing the bicistronic biosensors. Exploiting these approaches, we successfully demonstrated the release of ATP from the injured neurons and its extracellular diffusion in response to cellular injury in vitro and in vivo. Axotomy triggered intracellular calcium mobilization not only in the injured neuron but also in the intact neighboring cells, providing new insights into ATP's role as an injury signal. The tools developed in this study have demonstrated remarkable efficiency in unraveling the intricacies of ATP-mediated injury signaling.
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Affiliation(s)
- Asal Ghaffari Zaki
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Esra N Yiğit
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
| | - Mehmet Ş Aydın
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
| | - Emre Vatandaslar
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
- Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Emrah Eroglu
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
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5
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Otanuly M, Kubitschke M, Masseck OA. A Bright Future? A Perspective on Class C GPCR Based Genetically Encoded Biosensors. ACS Chem Neurosci 2024; 15:889-897. [PMID: 38380648 PMCID: PMC10921406 DOI: 10.1021/acschemneuro.3c00854] [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: 01/02/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
One of the major challenges in molecular neuroscience today is to accurately monitor neurotransmitters, neuromodulators, peptides, and various other biomolecules in the brain with high temporal and spatial resolution. Only a comprehensive understanding of neuromodulator dynamics, their release probability, and spatial distribution will unravel their ultimate role in cognition and behavior. This Perspective offers an overview of potential design strategies for class C GPCR-based biosensors. It briefly highlights current applications of GPCR-based biosensors, with a primary focus on class C GPCRs and their unique structural characteristics compared with other GPCR subfamilies. The discussion offers insights into plausible future design approaches for biosensor development targeting members of this specific GPCR subfamily. It is important to note that, at this stage, we are contemplating possibilities rather than presenting a concrete guide, as the pipeline is still under development.
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Affiliation(s)
- Margulan Otanuly
- Synthetische Biologie, Universität Bremen, Bremen 28359, Germany
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6
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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7
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Li SA, Meng XY, Zhang YJ, Chen CL, Jiao YX, Zhu YQ, Liu PP, Sun W. Progress in pH-Sensitive sensors: essential tools for organelle pH detection, spotlighting mitochondrion and diverse applications. Front Pharmacol 2024; 14:1339518. [PMID: 38269286 PMCID: PMC10806205 DOI: 10.3389/fphar.2023.1339518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
pH-sensitive fluorescent proteins have revolutionized the field of cellular imaging and physiology, offering insight into the dynamic pH changes that underlie fundamental cellular processes. This comprehensive review explores the diverse applications and recent advances in the use of pH-sensitive fluorescent proteins. These remarkable tools enable researchers to visualize and monitor pH variations within subcellular compartments, especially mitochondria, shedding light on organelle-specific pH regulation. They play pivotal roles in visualizing exocytosis and endocytosis events in synaptic transmission, monitoring cell death and apoptosis, and understanding drug effects and disease progression. Recent advancements have led to improved photostability, pH specificity, and subcellular targeting, enhancing their utility. Techniques for multiplexed imaging, three-dimensional visualization, and super-resolution microscopy are expanding the horizon of pH-sensitive protein applications. The future holds promise for their integration into optogenetics and drug discovery. With their ever-evolving capabilities, pH-sensitive fluorescent proteins remain indispensable tools for unravelling cellular dynamics and driving breakthroughs in biological research. This review serves as a comprehensive resource for researchers seeking to harness the potential of pH-sensitive fluorescent proteins.
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Affiliation(s)
- Shu-Ang Li
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Yan Meng
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Jie Zhang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Li Chen
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yu-Xue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Qing Zhu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pei-Pei Liu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Sun
- Department of Burn and Repair Reconstruction, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Kim M, Chen C, Yaari Z, Frederiksen R, Randall E, Wollowitz J, Cupo C, Wu X, Shah J, Worroll D, Lagenbacher RE, Goerzen D, Li YM, An H, Wang Y, Heller DA. Nanosensor-based monitoring of autophagy-associated lysosomal acidification in vivo. Nat Chem Biol 2023; 19:1448-1457. [PMID: 37322156 PMCID: PMC10721723 DOI: 10.1038/s41589-023-01364-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Autophagy is a cellular process with important functions that drive neurodegenerative diseases and cancers. Lysosomal hyperacidification is a hallmark of autophagy. Lysosomal pH is currently measured by fluorescent probes in cell culture, but existing methods do not allow for quantitative, transient or in vivo measurements. In the present study, we developed near-infrared optical nanosensors using organic color centers (covalent sp3 defects on carbon nanotubes) to measure autophagy-mediated endolysosomal hyperacidification in live cells and in vivo. The nanosensors localize to the lysosomes, where the emission band shifts in response to local pH, enabling spatial, dynamic and quantitative mapping of subtle changes in lysosomal pH. Using the sensor, we observed cellular and intratumoral hyperacidification on administration of mTORC1 and V-ATPase modulators, revealing that lysosomal acidification mirrors the dynamics of S6K dephosphorylation and LC3B lipidation while diverging from p62 degradation. This sensor enables the transient and in vivo monitoring of the autophagy-lysosomal pathway.
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Affiliation(s)
- Mijin Kim
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chen Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zvi Yaari
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Jaina Wollowitz
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christian Cupo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaojian Wu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Janki Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Worroll
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel E Lagenbacher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dana Goerzen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Yue-Ming Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Heeseon An
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Maryland NanoCenter, University of Maryland, College Park, MD, USA
| | - Daniel A Heller
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
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Chen Y, Pang S, Li J, Lu Y, Gao C, Xiao Y, Chen M, Wang M, Ren X. Genetically encoded protein sensors for metal ion detection in biological systems: a review and bibliometric analysis. Analyst 2023; 148:5564-5581. [PMID: 37872814 DOI: 10.1039/d3an01412f] [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: 10/25/2023]
Abstract
Metal ions are indispensable elements in living organisms and are associated with regulating various biological processes. An imbalance in metal ion content can lead to disorders in normal physiological functions of the human body and cause various diseases. Genetically encoded fluorescent protein sensors have the advantages of low biotoxicity, high specificity, and a long imaging time in vivo and have become a powerful tool to visualize or quantify the concentration level of biomolecules in vivo and in vitro, temporal and spatial distribution, and life activity process. This review analyzes the development status and current research hotspots in the field of genetically encoded fluorescent protein sensors by bibliometric analysis. Based on the results of bibliometric analysis, the research progress of genetically encoded fluorescent protein sensors for metal ion detection is reviewed, and the construction strategies, physicochemical properties, and applications of such sensors in biological imaging are summarized.
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Affiliation(s)
- Yuxueyuan Chen
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuChao Pang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Jingya Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yun Lu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chenxia Gao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanyu Xiao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Meiling Chen
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Meng Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin 301617, China
| | - Xiaoliang Ren
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
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10
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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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11
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Vu CQ, Arai S. Quantitative Imaging of Genetically Encoded Fluorescence Lifetime Biosensors. BIOSENSORS 2023; 13:939. [PMID: 37887132 PMCID: PMC10605767 DOI: 10.3390/bios13100939] [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: 09/05/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023]
Abstract
Genetically encoded fluorescence lifetime biosensors have emerged as powerful tools for quantitative imaging, enabling precise measurement of cellular metabolites, molecular interactions, and dynamic cellular processes. This review provides an overview of the principles, applications, and advancements in quantitative imaging with genetically encoded fluorescence lifetime biosensors using fluorescence lifetime imaging microscopy (go-FLIM). We highlighted the distinct advantages of fluorescence lifetime-based measurements, including independence from expression levels, excitation power, and focus drift, resulting in robust and reliable measurements compared to intensity-based approaches. Specifically, we focus on two types of go-FLIM, namely Förster resonance energy transfer (FRET)-FLIM and single-fluorescent protein (FP)-based FLIM biosensors, and discuss their unique characteristics and benefits. This review serves as a valuable resource for researchers interested in leveraging fluorescence lifetime imaging to study molecular interactions and cellular metabolism with high precision and accuracy.
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Affiliation(s)
- Cong Quang Vu
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Satoshi Arai
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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12
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Posner C, Mehta S, Zhang J. Fluorescent biosensor imaging meets deterministic mathematical modelling: quantitative investigation of signalling compartmentalization. J Physiol 2023; 601:4227-4241. [PMID: 37747358 PMCID: PMC10764149 DOI: 10.1113/jp282696] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Cells execute specific responses to diverse environmental cues by encoding information in distinctly compartmentalized biochemical signalling reactions. Genetically encoded fluorescent biosensors enable the spatial and temporal monitoring of signalling events in live cells. Temporal and spatiotemporal computational models can be used to interpret biosensor experiments in complex biochemical networks and to explore hypotheses that are difficult to test experimentally. In this review, we first provide brief discussions of the experimental toolkit of fluorescent biosensors as well as computational basics with a focus on temporal and spatiotemporal deterministic models. We then describe how we used this combined approach to identify and investigate a protein kinase A (PKA) - cAMP - Ca2+ oscillatory circuit in MIN6 β cells, a mouse pancreatic β cell system. We describe the application of this combined approach to interrogate how this oscillatory circuit is differentially regulated in a nano-compartment formed at the plasma membrane by the scaffolding protein A kinase anchoring protein 79/150. We leveraged both temporal and spatiotemporal deterministic models to identify the key regulators of this oscillatory circuit, which we confirmed with further experiments. The powerful approach of combining live-cell biosensor imaging with quantitative modelling, as discussed here, should find widespread use in the investigation of spatiotemporal regulation of cell signalling.
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Affiliation(s)
- Clara Posner
- Department of Pharmacology, University of California, San Diego, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
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13
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Pelletier R, Danylchuk DI, Benaissa H, Broch F, Vauchelles R, Gautier A, Klymchenko AS. Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles. Anal Chem 2023. [PMID: 37229557 DOI: 10.1021/acs.analchem.3c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.
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Affiliation(s)
- Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Hela Benaissa
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Fanny Broch
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Arnaud Gautier
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
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14
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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15
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Yang X, Li C, Li P, Fu Q. Ratiometric optical probes for biosensing. Theranostics 2023; 13:2632-2656. [PMID: 37215562 PMCID: PMC10196834 DOI: 10.7150/thno.82323] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/15/2023] [Indexed: 05/24/2023] Open
Abstract
Biosensing by optical probes is bringing about a revolution in our understanding of physiological and pathological states. Conventional optical probes for biosensing are prone to inaccurate detection results due to various analyte-independent factors that can lead to fluctuations in the absolute signal intensity. Ratiometric optical probes provide built-in self-calibration signal correction for more sensitive and reliable detection. Probes specifically developed for ratiometric optical detection have been shown to significantly improve the sensitivity and accuracy of biosensing. In this review, we focus on the advancements and sensing mechanism of ratiometric optical probes including photoacoustic (PA) probes, fluorescence (FL) probes, bioluminescence (BL) probes, chemiluminescence (CL) probes and afterglow probes. The versatile design strategies of these ratiometric optical probes are discussed along with a broad range of applications for biosensing such as sensing of pH, enzymes, reactive oxygen species (ROS), reactive nitrogen species (RNS), glutathione (GSH), metal ions, gas molecules and hypoxia factors, as well as the fluorescence resonance energy transfer (FRET)-based ratiometric probes for immunoassay biosensing. Finally, challenges and perspectives are discussed.
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16
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Nawaz H, Chen S, Zhang X, Li X, You T, Zhang J, Xu F. Cellulose-Based Fluorescent Material for Extreme pH Sensing and Smart Printing Applications. ACS NANO 2023; 17:3996-4008. [PMID: 36786234 DOI: 10.1021/acsnano.2c12846] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Environment-responsive fluorescence materials are being widely investigated for instrument-free determination of various environmental factors. However, developing an eco-friendly cellulose-based fluorescent pH sensor for sensing extreme acidity and alkalinity is still challenging. Herein, a highly fluorescent and multifunctional material is developed from biopolymer-based cellulose acetate. A biopolymer-based structure containing responsive functional groups such as -C═O and -NH is constructed by chemically bonding 5-amino-2,3-dihydrophthalazine-1,4-dione (luminol) onto cellulose acetate using 4,4'-diphenylmethane diisocyanate (MDI) as a cross-linking agent. The prepared material (Lum-MDI-CA) is characterized by UV-vis, Fourier transform infrared, 1H NMR, 13C NMR spectroscopies, and fluorescence techniques. The material exhibits excellent aqua blue fluorescence and demonstrates extreme pH sensing applications. Interesting results are further revealed after adding a pH-unresponsive dye such as MTPP as the reference to develop the ratiometric method. The ratiometric system clearly differentiates the extreme acidic pH 1 from pH 2 and extreme alkaline pH 12, 13, and 14 by visual and fluorescence color change response under a narrow pH range. In addition, the material is fabricated into transparent flexible fluorescent films which demonstrate an outstanding UV shielding, security printing, and haze properties for smart food packaging and printing applications.
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Affiliation(s)
- Haq Nawaz
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, China
| | - Sheng Chen
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, China
| | - Xun Zhang
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, China
| | - Xin Li
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, China
| | - Tingting You
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, China
| | - Jun Zhang
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Feng Xu
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, China
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17
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Zhou L, Yu Z, Zhang G, Jin Z, Zhang W, Qian J. Fluorescent "AND" logic gates for simultaneous detection of thiols and protons: photophysical properties, mechanism and bioimaging of living cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:818-828. [PMID: 36722868 DOI: 10.1039/d2ay01742c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Five fluorescent probes TP1-5 were demonstrated as two-input "AND" molecular logic gates for the detection of thiols and protons. The molecules were designed based on "thiol receptor-spacer1-fluorophore-spacer2-proton receptor" mode. The logic gates were constructed by employing maleimide, naphthalimide and morpholine (TP1-3)/N-methyl piperazine (TP4-5) as the thiol receptor, fluorophore and proton receptor, respectively. All probes show significant fluorescence enhancements upon addition of both protons and thiols. However, much weaker spectral responses were observed with the addition of only one single analyte. The fluorescence outputs, based on photoinduced electron transfer (PET) and (twisted) intramolecular charge transfer (TICT/ICT), were modulated by the proton receptor and linker. The length of spacer1 affects the responses toward thiols, whereas spacer2 influences the sensing performance toward protons. The difference between the pKa values of morpholine (∼5.80) and N-methyl piperazine (∼7.10) enables us to detect thiols in divergent pH circumstances. TP1-3 exhibit an excellent "AND" logic function for simultaneous detection of protons and thiols as well as bioimaging thiols in weakly acidic living cells. However, TP4 and TP5 are not good candidates for executing "AND" logic operation possibly due to the stronger electron donating properties and steric effect of N-methyl piperazine.
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Affiliation(s)
- Langping Zhou
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Zhihao Yu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Guangzhu Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Zechen Jin
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Junhong Qian
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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18
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Wagner TR, Burgstaller S, Frecot DI, Lukowski R, Rothbauer U. 30 Jahre Nanobodies: Neues von kleinen Helfern mit großem Potenzial. BIOSPEKTRUM : ZEITSCHRIFT DER GESELLSCHAFT FUR BIOLOGISHE CHEMIE (GBCH) UND DER VEREINIGUNG FUR ALLGEMEINE UND ANGEWANDTE MIKROBIOLOGIE (VAAM) 2023; 29:145-149. [PMID: 37073321 PMCID: PMC10101533 DOI: 10.1007/s12268-023-1900-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
2023 marks the 30th anniversary of the discovery of single-domain antibody fragments in camelids, better known as nanobodies. This was the starting point for their tremendous success story in biomedicine. Here we highlight recent advances in the development of nanobodies for the detection of neutralizing SARS-CoV-2 antibodies, as biosensors for monitoring extracellular metabolites and as tracer molecules for non-invasive imaging of immune cells.
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Affiliation(s)
- Teresa R. Wagner
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Pharmazeutische Biotechnologie, Markwiesenstraße 55, D-72770 Reutlingen, Deutschland
| | - Sandra Burgstaller
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- Pharmakologie, Toxikologie und Klinische Pharmazie, Universität Tübingen, Tübingen, Deutschland
| | - Desiree I. Frecot
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Pharmazeutische Biotechnologie, Markwiesenstraße 55, D-72770 Reutlingen, Deutschland
| | - Robert Lukowski
- Pharmakologie, Toxikologie und Klinische Pharmazie, Universität Tübingen, Tübingen, Deutschland
| | - Ulrich Rothbauer
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Pharmazeutische Biotechnologie, Markwiesenstraße 55, D-72770 Reutlingen, Deutschland
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19
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Yu W, Xu X, Jin K, Liu Y, Li J, Du G, Lv X, Liu L. Genetically encoded biosensors for microbial synthetic biology: From conceptual frameworks to practical applications. Biotechnol Adv 2023; 62:108077. [PMID: 36502964 DOI: 10.1016/j.biotechadv.2022.108077] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Genetically encoded biosensors are the vital components of synthetic biology and metabolic engineering, as they are regarded as powerful devices for the dynamic control of genotype metabolism and evolution/screening of desirable phenotypes. This review summarized the recent advances in the construction and applications of different genetically encoded biosensors, including fluorescent protein-based biosensors, nucleic acid-based biosensors, allosteric transcription factor-based biosensors and two-component system-based biosensors. First, the construction frameworks of these biosensors were outlined. Then, the recent progress of biosensor applications in creating versatile microbial cell factories for the bioproduction of high-value chemicals was summarized. Finally, the challenges and prospects for constructing robust and sophisticated biosensors were discussed. This review provided theoretical guidance for constructing genetically encoded biosensors to create desirable microbial cell factories for sustainable bioproduction.
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Affiliation(s)
- Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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20
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Comprehensive Investigation of Parameters Influencing Fluorescence Lifetime Imaging Microscopy in Frequency- and Time-Domain Illustrated by Phasor Plot Analysis. Int J Mol Sci 2022; 23:ijms232415885. [PMID: 36555522 PMCID: PMC9781030 DOI: 10.3390/ijms232415885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Having access to fluorescence lifetime, researchers can reveal in-depth details about the microenvironment as well as the physico-chemical state of the molecule under investigation. However, the high number of influencing factors might be an explanation for the strongly deviating values of fluorescent lifetimes for the same fluorophore reported in the literature. This could be the reason for the impression that inconsistent results are obtained depending on which detection and excitation scheme is used. To clarify this controversy, the two most common techniques for measuring fluorescence lifetimes in the time-domain and in the frequency-domain were implemented in one single microscopy setup and applied to a variety of fluorophores under different environmental conditions such as pH-value, temperature, solvent polarity, etc., along with distinct state forms that depend, for example, on the concentration. From a vast amount of measurement results, both setup- and sample-dependent parameters were extracted and represented using a single display form, the phasor-plot. The measurements showed consistent results between the two techniques and revealed which of the tested parameters has the strongest influence on the fluorescence lifetime. In addition, quantitative guidance as to which technique is most suitable for which research task and how to perform the experiment properly to obtain consistent fluorescence lifetimes is discussed.
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21
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Bell C, Multhoff J, Schwarzländer M. Biosensing on acid: fluorescent protein probes for low pH environments. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7199-7203. [PMID: 36478082 PMCID: PMC9730789 DOI: 10.1093/jxb/erac409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Christopher Bell
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Jan Multhoff
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
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22
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Curcic S, Erkan-Candag H, Pilic J, Malli R, Wiedner P, Tiapko O, Groschner K. TRPC3 governs the spatiotemporal organization of cellular Ca 2+ signatures by functional coupling to IP 3 receptors. Cell Calcium 2022; 108:102670. [PMID: 36375273 DOI: 10.1016/j.ceca.2022.102670] [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: 09/08/2022] [Revised: 10/12/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Communication between TRPC channels and IP3 receptors (IP3R) is considered pivotal in the generation of spatiotemporal Ca2+signaling patterns. Here we revisited the role of TRPC3-IP3R coupling for local Ca2+ signaling within TRPC3-harbouring micro/nanodomains using R-GECO as a reporter, fused to the channel´s C-terminus. Cytoplasmic Ca2+ changes at TRPC3 originated from both the entry of Ca2+ through the TRPC channel and Ca2+ mobilization via IP3R. Local Ca2+ changes at TRPC3 channels expressed in HEK293 cells were predominantly biphasic with IP3R-dependent initial Ca2+ transients, while exclusively monophasic signals were recorded when all three IP3R isoforms were lacking. Abrogation of Ca2+ entry through TRPC3 by point mutations, which impair Ca2+ permeability (E630Q), cation permeation (E630K), or DAG sensitivity (G652A), promoted microdomain Ca2+ oscillations. Ca2+ signals at E630Q, E630K, and G652A channels featured initial Ca2+ transients along with oscillatory activity. Similarly, when extracellular Ca2+ was omitted, IP3R-mediated Ca2+ transients and Ca2+ oscillations were promoted at the cytoplasmic face of wild-type TRPC3 channels. By contrast, oscillations, as well as initial Ca2+ transients, were virtually lacking, when the TRPC3 channels were sensitized by preexposure to low-level PLC activity. TIRF imaging provided evidence for dynamic colocalization of TRPC3 and IP3R. We suggest that TRPC3-mediated Ca2+ entry controls IP3R activity at ER-PM junctions to determine Ca2+ signaling signatures and enable specificity of downstream signaling.
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Affiliation(s)
- Sanja Curcic
- Gottfried-Schatz Research Center (Biophysics), Medical University of Graz, Austria.
| | - Hazel Erkan-Candag
- Gottfried-Schatz Research Center (Biophysics), Medical University of Graz, Austria
| | - Johannes Pilic
- Gottfried-Schatz Research Center (Molecular Biology and Biochemistry), Medical University of Graz, Austria
| | - Roland Malli
- Gottfried-Schatz Research Center (Molecular Biology and Biochemistry), Medical University of Graz, Austria
| | - Patrick Wiedner
- Gottfried-Schatz Research Center (Biophysics), Medical University of Graz, Austria
| | - Oleksandra Tiapko
- Gottfried-Schatz Research Center (Biophysics), Medical University of Graz, Austria
| | - Klaus Groschner
- Gottfried-Schatz Research Center (Biophysics), Medical University of Graz, Austria.
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23
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Mamontova AV, Simonyan TR, Bogdanov AM. Prospects of Genetically Encoded Flim Indicators for the Quantitative Assessment of Intracellular Parameters. Mol Biol 2022. [DOI: 10.1134/s0026893322050090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Moreau H, Gaillard I, Paris N. Genetically encoded fluorescent sensors adapted to acidic pH highlight subdomains within the plant cell apoplast. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6744-6757. [PMID: 35604912 DOI: 10.1093/jxb/erac210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Monitoring pH is one of the challenges in understanding diverse physiological regulations as well as ionic balance, especially in highly acidic environments such as the apoplast and the vacuole. To circumvent the poor efficiency of pH measurements below pH 5, we designed three genetically encoded sensors composed of two fluorescent proteins in tandem. We selected fluorescent protein pairs of low but sufficiently different pKa so that each protein could differentially sense the imposed pH. The generated tandems, named Acidin2, Acidin3, and Acidin4, were produced in Escherichia coli and extensively characterized. Altogether, these generated tandems cover a pH range of 3-8. The Acidins were targeted either for release in the apoplast (Apo) or for anchoring at the outer face of the plasma membrane (PM-Apo), with the fluorescent part exposed in the apoplast. Apoplastic Acidins in stably transformed Arabidopsis thaliana primary roots responded immediately and reversibly to pH changes, directly reporting physiological conditions related to cell elongation. In addition, membrane-anchored Acidins reveal a gradual acidification from the surface through the anticlinal wall of pavement cells, a process controlled at least partially by H+-ATPase activity.
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Affiliation(s)
- Hortense Moreau
- IPSiM, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Isabelle Gaillard
- IPSiM, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Nadine Paris
- IPSiM, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
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25
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IK Ca channels control breast cancer metabolism including AMPK-driven autophagy. Cell Death Dis 2022; 13:902. [PMID: 36302750 PMCID: PMC9613901 DOI: 10.1038/s41419-022-05329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/30/2022]
Abstract
Ca2+-activated K+ channels of intermediate conductance (IK) are frequently overexpressed in breast cancer (BC) cells, while IK channel depletion reduces BC cell proliferation and tumorigenesis. This raises the question, of whether and mechanistically how IK activity interferes with the metabolic activity and energy consumption rates, which are fundamental for rapidly growing cells. Using BC cells obtained from MMTV-PyMT tumor-bearing mice, we show that both, glycolysis and mitochondrial ATP-production are reduced in cells derived from IK-deficient breast tumors. Loss of IK altered the sub-/cellular K+- and Ca2+- homeostasis and mitochondrial membrane potential, ultimately resulting in reduced ATP-production and metabolic activity. Consequently, we find that BC cells lacking IK upregulate AMP-activated protein kinase activity to induce autophagy compensating the glycolytic and mitochondrial energy shortage. Our results emphasize that IK by modulating cellular Ca2+- and K+-dynamics contributes to the remodeling of metabolic pathways in cancer. Thus, targeting IK channel might disturb the metabolic activity of BC cells and reduce malignancy.
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26
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Simonyan TR, Protasova EA, Mamontova AV, Shakhov AM, Lukyanov KA, Maksimov EG, Bogdanov AM. A Single Fluorescent Protein-Based Indicator with a Time-Resolved Fluorescence Readout for Precise pH Measurements in the Alkaline Range. Int J Mol Sci 2022; 23:12907. [PMID: 36361706 PMCID: PMC9658282 DOI: 10.3390/ijms232112907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 09/19/2023] Open
Abstract
The real-time monitoring of the intracellular pH in live cells with high precision represents an important methodological challenge. Although genetically encoded fluorescent indicators can be considered as a probe of choice for such measurements, they are hindered mostly by the inability to determine an absolute pH value and/or a narrow dynamic range of the signal, making them inefficient for recording the small pH changes that typically occur within cellular organelles. Here, we study the pH sensitivity of a green-fluorescence-protein (GFP)-based emitter (EGFP-Y145L/S205V) with the alkaline-shifted chromophore's pKa and demonstrate that, in the pH range of 7.5-9.0, its fluorescence lifetime changes by a factor of ~3.5 in a quasi-linear manner in mammalian cells. Considering the relatively strong lifetime response in a narrow pH range, we proposed the mitochondria, which are known to have a weakly alkaline milieu, as a target for live-cell pH measurements. Using fluorescence lifetime imaging microscopy (FLIM) to visualize the HEK293T cells expressing mitochondrially targeted EGFP-Y145L/S205V, we succeeded in determining the absolute pH value of the mitochondria and recorded the ETC-uncoupler-stimulated pH shift with a precision of 0.1 unit. We thus show that a single GFP with alkaline-shifted pKa can act as a high-precision indicator that can be used in a specific pH range.
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Affiliation(s)
- Tatiana R. Simonyan
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Elena A. Protasova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Aleksander M. Shakhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Semenov Federal Research Center for Chemical Physics, 119991 Moscow, Russia
| | | | - Eugene G. Maksimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
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27
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Prabhu GRD, Yang TH, Shiu RT, Witek HA, Urban PL. Scanning pH-metry for Observing Reversibility in Protein Folding. Biochemistry 2022; 61:2377-2389. [PMID: 36251331 DOI: 10.1021/acs.biochem.2c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the main factors affecting protein structure in solution is pH. Traditionally, to study pH-dependent conformational changes in proteins, the concentration of the H+ ions is adjusted manually, complicating real-time analyses, hampering dynamic pH regulation, and consequently leading to a limited number of tested pH levels. Here, we present a programmable device, a scanning pH-meter, that can automatically generate different types of pH ramps and waveforms in a solution. A feedback loop algorithm calculates the required flow rates of the acid/base titrants, allowing one, for example, to generate periodic pH sine waveforms to study the reversibility of protein folding by fluorescence spectroscopy. Interestingly, for some proteins, the fluorescence intensity profiles recorded in such a periodically oscillating pH environment display hysteretic behavior indicating an asymmetry in the sequence of the protein unfolding/refolding events, which can most likely be attributed to their distinct kinetics. Another useful application of the scanning pH-meter concerns coupling it with an electrospray ionization mass spectrometer to observe pH-induced structural changes in proteins as revealed by their varying charge-state distributions. We anticipate a broad range of applications of the scanning pH-meter developed here, including protein folding studies, determination of the optimum pH for achieving maximum fluorescence intensity, and characterization of fluorescent dyes and other synthetic materials.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu300093, Taiwan
| | - Tzu-Hsin Yang
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
| | - Ruei-Tzung Shiu
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
| | - Henryk A Witek
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu300093, Taiwan
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu300093, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Sec 2, Kuang-Fu Road, Hsinchu300044, Taiwan
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28
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Li N, Zhang J, Wang M, Wang K, Liu J, Sun H, Su X. A pH-responsive ratiometric fluorescence system based on AIZS QDs and azamonardine for urea detection. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121431. [PMID: 35653812 DOI: 10.1016/j.saa.2022.121431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Herein, a ratiometric fluorescent nanoprobe was strategically fabricated using pH-sensitive azamonardine (Aza) as a pH indicator and pH-insensitive AIZS QDs as a reference fluorescence signal for urea activity determination and pH sensing. As the pH changed from 9.7 to 11.7, the resorcinol could react with dopamine to form the cyclization product (Aza), producing a fluorescence signal at 455 nm. Meanwhile, the fluorescence intensity of AIZS QDs at 566 nm remained unchanged. Thus, the ratio of the fluorescence intensity (F455/F566) was able to quantify pH value. Our designed pH-sensing platform showed a linear respond to pH values in the range of 9.7 to 11.7 at intervals of 0.2. In addition, the hydrolysis of urea by urease caused an increase of the system pH value, which can be used to measure the concentration of urea. The developed method for urea determination exhibited a good linear relationship from 0.02 to 20 mM and the limit of detection was 0.0103 mM. Moreover, the practical application was confirmed by urea analysis in real water sample with high feasibility and accuracy, indicating the great application prospects of this sensing platform for urea activity analysis.
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Affiliation(s)
- Ning Li
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China; Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jiabao Zhang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Mengjun Wang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Kaishuo Wang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jinying Liu
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Huilin Sun
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xingguang Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China.
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29
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Rennick JJ, Nowell CJ, Pouton CW, Johnston APR. Resolving subcellular pH with a quantitative fluorescent lifetime biosensor. Nat Commun 2022; 13:6023. [PMID: 36224168 PMCID: PMC9556823 DOI: 10.1038/s41467-022-33348-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 09/13/2022] [Indexed: 11/24/2022] Open
Abstract
Changes in sub-cellular pH play a key role in metabolism, membrane transport, and triggering cargo release from therapeutic delivery systems. Most methods to measure pH rely on intensity changes of pH sensitive fluorophores, however, these measurements are hampered by high uncertainty in the inferred pH and the need for multiple fluorophores. To address this, here we combine pH dependant fluorescent lifetime imaging microscopy (pHLIM) with deep learning to accurately quantify sub-cellular pH in individual vesicles. We engineer the pH sensitive protein mApple to localise in the cytosol, endosomes, and lysosomes, and demonstrate that pHLIM can rapidly detect pH changes induced by drugs such as bafilomycin A1 and chloroquine. We also demonstrate that polyethylenimine (a common transfection reagent) does not exhibit a proton sponge effect and had no measurable impact on the pH of endocytic vesicles. pHLIM is a simple and quantitative method that will help to understand drug action and disease progression. Measuring sub-cellular pH with high accuracy and spatiotemporal resolution remains challenging. Here, Johnston and co-workers develop a pH biosensor that combines the pH dependant fluorescent lifetime of mApple with deep learning to accurately determine sub-cellular pH in individual vesicles.
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Affiliation(s)
- Joshua J Rennick
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Cameron J Nowell
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Angus P R Johnston
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
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30
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Joy B, Cai Y, Bono DC, Sarkar D. Cell Rover-a miniaturized magnetostrictive antenna for wireless operation inside living cells. Nat Commun 2022; 13:5210. [PMID: 36138011 PMCID: PMC9499948 DOI: 10.1038/s41467-022-32862-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
An intracellular antenna can open up new horizons for fundamental and applied biology. Here, we introduce the Cell Rover, a magnetostrictive antenna which can operate wirelessly inside a living cell and is compatible with 3D biological systems. It is sub-mm in size, acoustically actuated by an AC magnetic field and resonantly operated at low MHz frequencies, which is ideal for living systems. We developed an injection scheme involving non-uniform magnetic fields for intracellular injection of the Cell Rovers and demonstrated their operation in fully opaque, stage VI Xenopus oocytes, for which real-time imaging with conventional technologies is challenging. We also show that they provide a pathway for multiplexing applications to individually address multiple cells or to tune to more than one antenna within the same cell for versatile functionalities. This technology forms the foundation stone that can enable the integration of future capabilities such as smart sensing, modulation as well as energy harvesting to power in-cell nanoelectronic computing and can potentially bring the prowess of information technology inside a living cell. This could lead to unprecedented opportunities for fundamental understanding of biology as well as diagnostics and therapeutics.
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Affiliation(s)
- Baju Joy
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yubin Cai
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David C Bono
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Deblina Sarkar
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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31
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Burgstaller S, Wagner TR, Bischof H, Bueckle S, Padamsey A, Frecot D, Kaiser PD, Skrabak D, Malli R, Lukowski R, Rothbauer U. Monitoring extracellular ion and metabolite dynamics with recombinant nanobody-fused biosensors. iScience 2022; 25:104907. [PMID: 36046190 PMCID: PMC9421384 DOI: 10.1016/j.isci.2022.104907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Ion and analyte changes in the tumor microenvironment (TME) alter the metabolic activity of cancer cells, promote tumor cell growth, and impair anti-tumor immunity. Consequently, accurate determination and visualization of extracellular changes of analytes in real time is desired. In this study, we genetically combined FRET-based biosensors with nanobodies (Nbs) to specifically visualize and monitor extracellular changes in K+, pH, and glucose on cell surfaces. We demonstrated that these Nb-fused biosensors quantitatively visualized K+ alterations on cancer and non-cancer cell lines and primary neurons. By implementing a HER2-specific Nb, we generated functional K+ and pH sensors, which specifically stained HER2-positive breast cancer cells. Based on the successful development of several Nb-fused biosensor combinations, we anticipate that this approach can be readily extended to other biosensors and will open new opportunities for the study of extracellular analytes in advanced experimental settings. Generation of recombinant nanobody-fused FRET biosensors Nb-fused biosensors specifically bind targets on the outer surface of various cells Cellular bound Nb-biosensors visualize extracellular analyte changes in real time
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Affiliation(s)
- Sandra Burgstaller
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Helmut Bischof
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Sarah Bueckle
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Aman Padamsey
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Desiree Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - David Skrabak
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Roland Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
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32
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Prat Castro S, Kudrina V, Jaślan D, Böck J, Scotto Rosato A, Grimm C. Neurodegenerative Lysosomal Storage Disorders: TPC2 Comes to the Rescue! Cells 2022; 11:cells11182807. [PMID: 36139381 PMCID: PMC9496660 DOI: 10.3390/cells11182807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022] Open
Abstract
Lysosomal storage diseases (LSDs) resulting from inherited gene mutations constitute a family of disorders that disturb lysosomal degradative function leading to abnormal storage of macromolecular substrates. In most LSDs, central nervous system (CNS) involvement is common and leads to the progressive appearance of neurodegeneration and early death. A growing amount of evidence suggests that ion channels in the endolysosomal system play a crucial role in the pathology of neurodegenerative LSDs. One of the main basic mechanisms through which the endolysosomal ion channels regulate the function of the endolysosomal system is Ca2+ release, which is thought to be essential for intracellular compartment fusion, fission, trafficking and lysosomal exocytosis. The intracellular TRPML (transient receptor potential mucolipin) and TPC (two-pore channel) ion channel families constitute the main essential Ca2+-permeable channels expressed on endolysosomal membranes, and they are considered potential drug targets for the prevention and treatment of LSDs. Although TRPML1 activation has shown rescue effects on LSD phenotypes, its activity is pH dependent, and it is blocked by sphingomyelin accumulation, which is characteristic of some LSDs. In contrast, TPC2 activation is pH-independent and not blocked by sphingomyelin, potentially representing an advantage over TRPML1. Here, we discuss the rescue of cellular phenotypes associated with LSDs such as cholesterol and lactosylceramide (LacCer) accumulation or ultrastructural changes seen by electron microscopy, mediated by the small molecule agonist of TPC2, TPC2-A1-P, which promotes lysosomal exocytosis and autophagy. In summary, new data suggest that TPC2 is a promising target for the treatment of different types of LSDs such as MLIV, NPC1, and Batten disease, both in vitro and in vivo.
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Affiliation(s)
| | | | | | | | | | - Christian Grimm
- Correspondence: (A.S.R.); (C.G.); Tel.: +49-89-2180-73811 (C.G.)
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33
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Koda K, Keller S, Kojima R, Kamiya M, Urano Y. Measuring the pH of Acidic Vesicles in Live Cells with an Optimized Fluorescence Lifetime Imaging Probe. Anal Chem 2022; 94:11264-11271. [PMID: 35913787 DOI: 10.1021/acs.analchem.2c01840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acidification of intracellular vesicles, such as endosomes and lysosomes, is a key pathway for regulating the function of internal proteins. Most conventional methods of measuring pH are not satisfactory for quantifying the pH inside these vesicles. Here, we investigated the molecular requirements for a fluorescence probe to measure the intravesicular acidic pH in living cells by means of fluorescence lifetime imaging microscopy (FLIM). The developed probe, m-DiMeNAF488, exhibits a pH-dependent equilibrium between highly fluorescent and moderately fluorescent forms, which has distinct and detectable fluorescence lifetimes of 4.36 and 0.58 ns, respectively. The pKa(τ) value of m-DiMeNAF488 was determined to be 4.58, which would be favorable for evaluating the pH in the acidic vesicles. We were able to monitor the pH changes in phagosomes during phagocytosis by means of FLIM using m-DiMeNAF488. This probe is expected to be a useful tool for investigating acidic pH-regulated biological phenomena.
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Affiliation(s)
| | | | - Ryosuke Kojima
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mako Kamiya
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yasuteru Urano
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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34
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Towards 'end-to-end' analysis and understanding of biological timecourse data. Biochem J 2022; 479:1257-1263. [PMID: 35713413 PMCID: PMC9246344 DOI: 10.1042/bcj20220053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022]
Abstract
Petabytes of increasingly complex and multidimensional live cell and tissue imaging data are generated every year. These videos hold large promise for understanding biology at a deep and fundamental level, as they capture single-cell and multicellular events occurring over time and space. However, the current modalities for analysis and mining of these data are scattered and user-specific, preventing more unified analyses from being performed over different datasets and obscuring possible scientific insights. Here, we propose a unified pipeline for storage, segmentation, analysis, and statistical parametrization of live cell imaging datasets.
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35
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Wu SY, Shen Y, Shkolnikov I, Campbell RE. Fluorescent Indicators For Biological Imaging of Monatomic Ions. Front Cell Dev Biol 2022; 10:885440. [PMID: 35573682 PMCID: PMC9093666 DOI: 10.3389/fcell.2022.885440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Monatomic ions play critical biological roles including maintaining the cellular osmotic pressure, transmitting signals, and catalyzing redox reactions as cofactors in enzymes. The ability to visualize monatomic ion concentration, and dynamic changes in the concentration, is essential to understanding their many biological functions. A growing number of genetically encodable and synthetic indicators enable the visualization and detection of monatomic ions in biological systems. With this review, we aim to provide a survey of the current landscape of reported indicators. We hope this review will be a useful guide to researchers who are interested in using indicators for biological applications and to tool developers seeking opportunities to create new and improved indicators.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Irene Shkolnikov
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
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36
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Karsten L, Goett-Zink L, Schmitz J, Hoffrogge R, Grünberger A, Kottke T, Müller KM. Genetically Encoded Ratiometric pH Sensors for the Measurement of Intra- and Extracellular pH and Internalization Rates. BIOSENSORS 2022; 12:bios12050271. [PMID: 35624572 PMCID: PMC9138566 DOI: 10.3390/bios12050271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
pH-sensitive fluorescent proteins as genetically encoded pH sensors are promising tools for monitoring intra- and extracellular pH. However, there is a lack of ratiometric pH sensors, which offer a good dynamic range and can be purified and applied extracellularly to investigate uptake. In our study, the bright fluorescent protein CoGFP_V0 was C-terminally fused to the ligand epidermal growth factor (EGF) and retained its dual-excitation and dual-emission properties as a purified protein. The tandem fluorescent variants EGF-CoGFP-mTagBFP2 (pK′ = 6.6) and EGF-CoGFP-mCRISPRed (pK′ = 6.1) revealed high dynamic ranges between pH 4.0 and 7.5. Using live-cell fluorescence microscopy, both pH sensor molecules permitted the conversion of fluorescence intensity ratios to detailed intracellular pH maps, which revealed pH gradients within endocytic vesicles. Additionally, extracellular binding of the pH sensors to cells expressing the EGF receptor (EGFR) enabled the tracking of pH shifts inside cultivation chambers of a microfluidic device. Furthermore, the dual-emission properties of EGF-CoGFP-mCRISPRed upon 488 nm excitation make this pH sensor a valuable tool for ratiometric flow cytometry. This high-throughput method allowed for the determination of internalization rates, which represents a promising kinetic parameter for the in vitro characterization of protein–drug conjugates in cancer therapy.
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Affiliation(s)
- Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Lukas Goett-Zink
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Raimund Hoffrogge
- Cell Culture Technology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
- Correspondence:
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Burgstaller S, Bischof H, Matt L, Lukowski R. Assessing K + ions and K + channel functions in cancer cell metabolism using fluorescent biosensors. Free Radic Biol Med 2022; 181:43-51. [PMID: 35091062 DOI: 10.1016/j.freeradbiomed.2022.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Cancer represents a leading cause of death worldwide. Hence, a better understanding of the molecular mechanisms causing and propelling the disease is of utmost importance. Several cancer entities are associated with altered K+ channel expression which is frequently decisive for malignancy and disease outcome. The impact of such oncogenic K+ channels on cell patho-/physiology and homeostasis and their roles in different subcellular compartments is, however, far from being understood. A refined method to simultaneously investigate metabolic and ionic signaling events on the level of individual cells and their organelles represent genetically encoded fluorescent biosensors, that allow a high-resolution investigation of compartmentalized metabolite or ion dynamics in a non-invasive manner. This feature of these probes makes them versatile tools to visualize and understand subcellular consequences of aberrant K+ channel expression and activity in K+ channel related cancer research.
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Affiliation(s)
- Sandra Burgstaller
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, 72770, Germany.
| | - Helmut Bischof
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany
| | - Lucas Matt
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany.
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Shimolina L, Potekhina E, Druzhkova I, Lukina M, Dudenkova V, Belousov V, Shcheslavskiy V, Zagaynova E, Shirmanova M. Fluorescence lifetime-based pH mapping of tumors in vivo using new genetically encoded sensor SypHerRed. Biophys J 2022; 121:1156-1165. [PMID: 35218737 PMCID: PMC9034243 DOI: 10.1016/j.bpj.2022.02.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
Changes in intracellular pH (pHi) reflect metabolic states of cancer cells during tumor growth and dissemination. Therefore, monitoring of pH is essential for understanding the metabolic mechanisms that support cancer progression. Genetically encoded fluorescent pH sensors have become irreplaceable tools for real-time tracking pH in particular subcellular compartments of living cells. However, ratiometric readout of most of the pH probes is poorly suitable to measure pH in thick samples ex vivo or tissues in vivo including solid tumors. Fluorescence lifetime imaging (FLIM) is a promising alternative to the conventional fluorescent microscopy as it much less depends on light scattering in thick samples. Here, we present a quantitative approach to map intracellular pH in cancer cells and tumors in vivo, relying on fluorescence lifetime readout of a genetically encoded pH sensor SypHerRed. We demonstrate the utility of SypHerRed in visualizing pHi in cancer cell culture and in mouse tumor xenografts using FLIM-microscopy and macroscopy. For the first time, the absolute pHi value is obtained for tumors in vivo by an optical technique. In addition, we demonstrate the possibility of simultaneous detection of pH and endogenous fluorescence of metabolic cofactor NADH, which provides a complementary insight into metabolic aspects of cancer. Fluorescence lifetime-based readout and red-shifted spectra make pH sensor SypHerRed a promising instrument for multiparameter in vivo imaging applications.
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Affiliation(s)
- Liubov Shimolina
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia; Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Ekaterina Potekhina
- Pirogov Russian National Research Medical University, Laboratory of Experimental Oncology, Moscow, Russia
| | - Irina Druzhkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria Lukina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Varvara Dudenkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Vsevolod Belousov
- Pirogov Russian National Research Medical University, Laboratory of Experimental Oncology, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav Shcheslavskiy
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia; Becker&Hickl GmbH, Nunsdorfer Ring 7-9, 12277 Berlin, Germany.
| | - Elena Zagaynova
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Marina Shirmanova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.
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Ponomareva D, Petukhova E, Bregestovski P. Simultaneous Monitoring of pH and Chloride (Cl -) in Brain Slices of Transgenic Mice. Int J Mol Sci 2021; 22:13601. [PMID: 34948398 PMCID: PMC8708776 DOI: 10.3390/ijms222413601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Optosensorics is the direction of research possessing the possibility of non-invasive monitoring of the concentration of intracellular ions or activity of intracellular components using specific biosensors. In recent years, genetically encoded proteins have been used as effective optosensory means. These probes possess fluorophore groups capable of changing fluorescence when interacting with certain ions or molecules. For monitoring of intracellular concentrations of chloride ([Cl-]i) and hydrogen ([H+] i) the construct, called ClopHensor, which consists of a H+- and Cl--sensitive variant of the enhanced green fluorescent protein (E2GFP) fused with a monomeric red fluorescent protein (mDsRed) has been proposed. We recently developed a line of transgenic mice expressing ClopHensor in neurons and obtained the map of its expression in different areas of the brain. The purpose of this study was to examine the effectiveness of transgenic mice expressing ClopHensor for estimation of [H+]i and [Cl-]i concentrations in neurons of brain slices. We performed simultaneous monitoring of [H+]i and [Cl-]i under different experimental conditions including changing of external concentrations of ions (Ca2+, Cl-, K+, Na+) and synaptic stimulation of Shaffer's collaterals of hippocampal slices. The results obtained illuminate different pathways of regulation of Cl- and pH equilibrium in neurons and demonstrate that transgenic mice expressing ClopHensor represent a reliable tool for non-invasive simultaneous monitoring of intracellular Cl- and pH.
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Affiliation(s)
- Daria Ponomareva
- Institut de Neurosciences des Systèmes, Aix-Marseille University, INSERM, INS, 13005 Marseille, France;
- Institute of Neurosciences, Kazan State Medical University, 420111 Kazan, Russia;
- Department of Normal Physiology, Kazan State Medical University, 420111 Kazan, Russia
| | - Elena Petukhova
- Institute of Neurosciences, Kazan State Medical University, 420111 Kazan, Russia;
- Department of Normal Physiology, Kazan State Medical University, 420111 Kazan, Russia
| | - Piotr Bregestovski
- Institut de Neurosciences des Systèmes, Aix-Marseille University, INSERM, INS, 13005 Marseille, France;
- Institute of Neurosciences, Kazan State Medical University, 420111 Kazan, Russia;
- Department of Normal Physiology, Kazan State Medical University, 420111 Kazan, Russia
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41
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Colaruotolo LA, Peters E, Corradini MG. Novel luminescent techniques in aid of food quality, product development, and food processing. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Erdogan YC, Altun HY, Secilmis M, Ata BN, Sevimli G, Cokluk Z, Zaki AG, Sezen S, Akgul Caglar T, Sevgen İ, Steinhorn B, Ai H, Öztürk G, Belousov VV, Michel T, Eroglu E. Complexities of the chemogenetic toolkit: Differential mDAAO activation by d-amino substrates and subcellular targeting. Free Radic Biol Med 2021; 177:132-142. [PMID: 34687864 PMCID: PMC8639799 DOI: 10.1016/j.freeradbiomed.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023]
Abstract
A common approach to investigate oxidant-regulated intracellular pathways is to add exogenous H2O2 to living cells or tissues. However, the addition of H2O2 to the culture medium of cells or tissues approach does not accurately replicate intracellular redox-mediated cell responses. d-amino acid oxidase (DAAO)-based chemogenetic tools represent informative methodological advances that permit the generation of H2O2 on demand with a high spatiotemporal resolution by providing or withdrawing the DAAO substrate d-amino acids. Much has been learned about the intracellular transport of H2O2 through studies using DAAO, yet these valuable tools remain incompletely characterized in many cultured cells. In this study, we describe and characterize in detail the features of a new modified variant of DAAO (termed mDAAO) with improved catalytic activities. We tested mDAAO functionality in several cultured cell lines employing live-cell imaging techniques. Our imaging experiments show that mDAAO is suitable for the generation of H2O2 under hypoxic conditions imaged with the novel ultrasensitive H2O2 sensor (HyPer7). Moreover, this approach was suitable for generating H2O2 in a reversible and concentration-dependent manner in subcellular locales. Furthermore, we show that the choice of d-amino acids differentially affects mDAAO-dependent intracellular H2O2 generation. When paired with the hydrogen sulfide (H2S) sensor hsGFP, administration of the sulfur-containing amino acid d-cysteine to cells expressing mDAAO generates robust H2S signals. We also show that chemogenetic H2O2 generation in different cell types yields distinct HyPer7 profiles. These studies fully characterize the new mDAAO as a novel chemogenetic tool and provide multiparametric approaches for cell manipulation that may open new lines of investigations for redox biochemists to dissect the role of ROS signaling pathways with high spatial and temporal precision.
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Affiliation(s)
- Yusuf C Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hamza Y Altun
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Busra N Ata
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Serap Sezen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Tuba Akgul Caglar
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - İlker Sevgen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Benjamin Steinhorn
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Huiwang Ai
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Physiology Department, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Vsevelod V Belousov
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Institute of Cardiovascular Physiology, Universitätsmedizin Göttingen, 37073, Göttingen, Germany
| | - Thomas Michel
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey; Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Austria; Nanotechnology Research and Application Center, Sabanci University, Istanbul, Turkey.
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43
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Podinovskaia M, Prescianotto-Baschong C, Buser DP, Spang A. A novel live-cell imaging assay reveals regulation of endosome maturation. eLife 2021; 10:e70982. [PMID: 34846303 PMCID: PMC8635980 DOI: 10.7554/elife.70982] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
Cell-cell communication is an essential process in life, with endosomes acting as key organelles for regulating uptake and secretion of signaling molecules. Endocytosed material is accepted by the sorting endosome where it either is sorted for recycling or remains in the endosome as it matures to be degraded in the lysosome. Investigation of the endosome maturation process has been hampered by the small size and rapid movement of endosomes in most cellular systems. Here, we report an easy versatile live-cell imaging assay to monitor endosome maturation kinetics, which can be applied to a variety of mammalian cell types. Acute ionophore treatment led to enlarged early endosomal compartments that matured into late endosomes and fused with lysosomes to form endolysosomes. Rab5-to-Rab7 conversion and PI(3)P formation and turn over were recapitulated with this assay and could be observed with a standard widefield microscope. We used this approach to show that Snx1 and Rab11-positive recycling endosome recruitment occurred throughout endosome maturation and was uncoupled from Rab conversion. In contrast, efficient endosomal acidification was dependent on Rab conversion. The assay provides a powerful tool to further unravel various aspects of endosome maturation.
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Affiliation(s)
| | | | | | - Anne Spang
- Biozentrum, University of BaselBaselSwitzerland
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44
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Yapici N, Gao X, Yan X, Hou S, Jockusch S, Lesniak L, Gibson KM, Bi L. Novel Dual-Organelle-Targeting Probe (RCPP) for Simultaneous Measurement of Organellar Acidity and Alkalinity in Living Cells. ACS OMEGA 2021; 6:31447-31456. [PMID: 34869971 PMCID: PMC8637586 DOI: 10.1021/acsomega.1c03087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/01/2021] [Indexed: 05/06/2023]
Abstract
Many organelles, such as lysosomes and mitochondria, maintain a pH that is different from the cytoplasmic pH. These pH differences have important functional ramifications for those organelles. Many cellular events depend upon a well-compartmentalized distribution of H+ ions spanning the membrane for the optimal function. Cells have developed a variety of mechanisms that enable the regulation of organelle pH. However, the measurement of organellar acidity/alkalinity in living cells has remained a challenge. Currently, most existing probes for the estimation of intracellular pH show a single -organelle targeting capacity. Such probes provide data that fails to comprehensively reveal the pathological and physiological roles and connections between mitochondria and lysosomes in different species. Mitochondrial and lysosomal functions are closely related and important for regulating cellular homeostasis. Accordingly, the design of a single fluorescent probe that can simultaneously target mitochondria and lysosomes is highly desirable, enabling a better understanding of the crosstalk between these organelles. We report the development of a novel fluorescent sensor, rhodamine-coumarin pH probe (RCPP), for detection of organellar acidity/alkalinity. RCPP simultaneously moves between mitochondrion and lysosome subcellular locations, facilitating the simultaneous monitoring of pH alterations in mitochondria and lysosomes.
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Affiliation(s)
- Nazmiye
B. Yapici
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Xiang Gao
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Xin Yan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shanshan Hou
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Steffen Jockusch
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Lillian Lesniak
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - K. Michael Gibson
- Department
of Pharmacotherapy, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Lanrong Bi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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Burgstaller S, Bischof H, Rauter T, Schmidt T, Schindl R, Patz S, Groschup B, Filser S, van den Boom L, Sasse P, Lukowski R, Plesnila N, Graier WF, Malli R. Immobilization of Recombinant Fluorescent Biosensors Permits Imaging of Extracellular Ion Signals. ACS Sens 2021; 6:3994-4000. [PMID: 34752056 PMCID: PMC8630794 DOI: 10.1021/acssensors.1c01369] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Given the importance
of ion gradients and fluxes in biology, monitoring
ions locally at the exterior of the plasma membrane of intact cells
in a noninvasive manner is highly desirable but challenging. Classical
targeting of genetically encoded biosensors at the exterior of cell
surfaces would be a suitable approach; however, it often leads to
intracellular accumulation of the tools in vesicular structures and
adverse modifications, possibly impairing sensor functionality. To
tackle these issues, we generated recombinant fluorescent ion biosensors
fused to traptavidin (TAv) specifically coupled to a biotinylated
AviTag expressed on the outer cell surface of cells. We show that
purified chimeras of TAv and pH-Lemon or GEPII 1.0, Förster
resonance energy transfer-based pH and K+ biosensors, can
be immobilized directly and specifically on biotinylated surfaces
including glass platelets and intact cells, thereby remaining fully
functional for imaging of ion dynamics. The immobilization of recombinant
TAv–GEPII 1.0 on the extracellular cell surface of primary
cortical rat neurons allowed imaging of excitotoxic glutamate-induced
K+ efflux in vitro. We also performed micropatterning of
purified TAv biosensors using a microperfusion system to generate
spatially separated TAv–pH-Lemon and TAv–GEPII 1.0 spots
for simultaneous pH and K+ measurements on cell surfaces.
Our results suggest that the approach can be greatly expanded by immobilizing
various biosensors on extracellular surfaces to quantitatively visualize
microenvironmental transport and signaling processes in different
cell culture models and other experimental settings.
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Affiliation(s)
- Sandra Burgstaller
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Helmut Bischof
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany
| | - Thomas Rauter
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
| | - Tony Schmidt
- Gottfried Schatz Research Center, Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
| | - Rainer Schindl
- Gottfried Schatz Research Center, Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
| | - Silke Patz
- Department of Neurosurgery, Medical University of Graz, Auenbruggerplatz 29, Graz 8036, Austria
| | - Bernhard Groschup
- Laboratory of Experimental Stroke Research, Institute for Stroke and Dementia Research, University of Munich Medical Center, Munich 81377, Germany
| | - Severin Filser
- Laboratory of Experimental Stroke Research, Institute for Stroke and Dementia Research, University of Munich Medical Center, Munich 81377, Germany
| | - Lucas van den Boom
- Institute of Physiology I, Medical Faculty, University of Bonn, Bonn 53127, Germany
| | - Philipp Sasse
- Institute of Physiology I, Medical Faculty, University of Bonn, Bonn 53127, Germany
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany
| | - Nikolaus Plesnila
- Laboratory of Experimental Stroke Research, Institute for Stroke and Dementia Research, University of Munich Medical Center, Munich 81377, Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, Munich 81377, Germany
| | - Wolfgang F. Graier
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
- BioTechMed Graz, Mozartgasse 12/II, Graz 8010, Austria
| | - Roland Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, Graz 8010, Austria
- BioTechMed Graz, Mozartgasse 12/II, Graz 8010, Austria
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46
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Moreau H, Zimmermann SD, Gaillard I, Paris N. pH biosensing in the plant apoplast-a focus on root cell elongation. PLANT PHYSIOLOGY 2021; 187:504-514. [PMID: 35237817 PMCID: PMC8491080 DOI: 10.1093/plphys/kiab313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/19/2021] [Indexed: 05/24/2023]
Abstract
The pH parameter of soil plays a key role for plant nutrition as it is affecting the availability of minerals and consequently determines plant growth. Although the mechanisms by which root perceive the external pH is still unknown, the impact of external pH on tissue growth has been widely studied especially in hypocotyl and root. Thanks to technological development of cell imaging and fluorescent sensors, we can now monitor pH in real time with at subcellular definition. In this focus, fluorescent dye-based, as well as genetically-encoded pH indicators are discussed especially with respect to their ability to monitor acidic pH in the context of primary root. The notion of apoplastic subdomains is discussed and suggestions are made to develop fluorescent indicators for pH values below 5.0.
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Affiliation(s)
- Hortense Moreau
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Isabelle Gaillard
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Nadine Paris
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
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Secilmis M, Altun HY, Pilic J, Erdogan YC, Cokluk Z, Ata BN, Sevimli G, Zaki AG, Yigit EN, Öztürk G, Malli R, Eroglu E. A Co-Culture-Based Multiparametric Imaging Technique to Dissect Local H 2O 2 Signals with Targeted HyPer7. BIOSENSORS 2021; 11:338. [PMID: 34562927 PMCID: PMC8466187 DOI: 10.3390/bios11090338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/19/2023]
Abstract
Multispectral live-cell imaging is an informative approach that permits detecting biological processes simultaneously in the spatial and temporal domain by exploiting spectrally distinct biosensors. However, the combination of fluorescent biosensors with distinct spectral properties such as different sensitivities, and dynamic ranges can undermine accurate co-imaging of the same analyte in different subcellular locales. We advanced a single-color multiparametric imaging method, which allows simultaneous detection of hydrogen peroxide (H2O2) in multiple cell locales (nucleus, cytosol, mitochondria) using the H2O2 biosensor HyPer7. Co-culturing of endothelial cells stably expressing differentially targeted HyPer7 biosensors paved the way for co-imaging compartmentalized H2O2 signals simultaneously in neighboring cells in a single experimental setup. We termed this approach COMPARE IT, which is an acronym for co-culture-based multiparametric imaging technique. Employing this approach, we detected lower H2O2 levels in mitochondria of endothelial cells compared to the cell nucleus and cytosol under basal conditions. Upon administering exogenous H2O2, the cytosolic and nuclear-targeted probes displayed similarly slow and moderate HyPer7 responses, whereas the mitochondria-targeted HyPer7 signal plateaued faster and reached higher amplitudes. Our results indicate striking differences in mitochondrial H2O2 accumulation of endothelial cells. Here, we present the method's potential as a practicable and informative multiparametric live-cell imaging technique.
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Affiliation(s)
- Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Hamza Yusuf Altun
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Johannes Pilic
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Yusuf Ceyhun Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Busra Nur Ata
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Esra Nur Yigit
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Department of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Physiology Department, International School of Medicine, Istanbul Medipol University, 34810 Istanbul, Turkey
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Nanotechnology Research and Application Center, Sabanci University, 34956 Istanbul, Turkey
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48
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Stellon D, Tran MTN, Talbot J, Chear S, Khalid MKNM, Pébay A, Vickers JC, King AE, Hewitt AW, Cook AL. CRISPR/Cas-Mediated Knock-in of Genetically Encoded Fluorescent Biosensors into the AAVS1 Locus of Human-Induced Pluripotent Stem Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2549:379-398. [PMID: 34505269 DOI: 10.1007/7651_2021_422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded fluorescent biosensors (GEFBs) enable researchers to visualize and quantify cellular processes in live cells. Induced pluripotent stem cells (iPSCs) can be genetically engineered to express GEFBs via integration into the Adeno-Associated Virus Integration Site 1 (AAVS1) safe harbor locus. This can be achieved using CRISPR/Cas ribonucleoprotein targeting to cause a double-strand break at the AAVS1 locus, which subsequently undergoes homology-directed repair (HDR) in the presence of a donor plasmid containing the GEFB sequence. We describe an optimized protocol for CRISPR/Cas-mediated knock-in of GEFBs into the AAVS1 locus of human iPSCs that allows puromycin selection and which exhibits negligible off-target editing. The resulting iPSC lines can be differentiated into cells of different lineages while retaining expression of the GEFB, enabling live-cell interrogation of cell pathway activities across a diversity of disease models.
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Affiliation(s)
- David Stellon
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia.
| | | | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | | | - Alice Pébay
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia.,Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia.
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49
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Van Genechten W, Van Dijck P, Demuyser L. Fluorescent toys 'n' tools lighting the way in fungal research. FEMS Microbiol Rev 2021; 45:fuab013. [PMID: 33595628 PMCID: PMC8498796 DOI: 10.1093/femsre/fuab013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
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Affiliation(s)
- Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200g, 3001 Leuven-Heverlee, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
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50
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Vu CQ, Fukushima SI, Wazawa T, Nagai T. A highly-sensitive genetically encoded temperature indicator exploiting a temperature-responsive elastin-like polypeptide. Sci Rep 2021; 11:16519. [PMID: 34389773 PMCID: PMC8363741 DOI: 10.1038/s41598-021-96049-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
Genetically encoded temperature indicators (GETIs) allow for real-time measurement of subcellular temperature dynamics in live cells. However, GETIs have suffered from poor temperature sensitivity, which may not be sufficient to resolve small heat production from a biological process. Here, we develop a highly-sensitive GETI, denoted as ELP-TEMP, comprised of a temperature-responsive elastin-like polypeptide (ELP) fused with a cyan fluorescent protein (FP), mTurquoise2 (mT), and a yellow FP, mVenus (mV), as the donor and acceptor, respectively, of Förster resonance energy transfer (FRET). At elevated temperatures, the ELP moiety in ELP-TEMP undergoes a phase transition leading to an increase in the FRET efficiency. In HeLa cells, ELP-TEMP responded to the temperature from 33 to 40 °C with a maximum temperature sensitivity of 45.1 ± 8.1%/°C, which was the highest ever temperature sensitivity among hitherto-developed fluorescent nanothermometers. Although ELP-TEMP showed sensitivity not only to temperature but also to macromolecular crowding and self-concentration, we were able to correct the output of ELP-TEMP to achieve accurate temperature measurements at a subcellular resolution. We successfully applied ELP-TEMP to accurately measure temperature changes in cells induced by a local heat spot, even if the temperature difference was as small as < 1 °C, and to visualize heat production from stimulated Ca2+ influx in live HeLa cells induced by a chemical stimulation. Furthermore, we investigated temperatures in the nucleus and cytoplasm of live HeLa cells and found that their temperatures were almost the same within the temperature resolution of our measurement. Our study would contribute to better understanding of cellular temperature dynamics, and ELP-TEMP would be a useful GETI for the investigation of cell thermobiology.
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Affiliation(s)
- Cong Quang Vu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.,SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Shun-Ichi Fukushima
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Tetsuichi Wazawa
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Takeharu Nagai
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan. .,SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan.
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