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Call DH, Adjei JA, Pilgrim R, Jeong JW, Willis EV, Zegarra RA, Tapia NL, Osterhaus M, Vance JA, Voyton CM, Call JA, Pizarro SS, Morris JC, Christensen KA. A multiplexed high throughput screening assay using flow cytometry identifies glycolytic molecular probes in bloodstream form Trypanosoma brucei. Int J Parasitol Drugs Drug Resist 2024; 26:100557. [PMID: 39163740 PMCID: PMC11381906 DOI: 10.1016/j.ijpddr.2024.100557] [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: 04/04/2024] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024]
Abstract
Kinetoplastid organisms, including Trypanosoma brucei, are a significant health burden in many tropical and semitropical countries. Much of their metabolism is poorly understood. To better study kinetoplastid metabolism, chemical probes that inhibit kinetoplastid enzymes are needed. To discover chemical probes, we have developed a high-throughput flow cytometry screening assay that simultaneously measures multiple glycolysis-relevant metabolites in live T. brucei bloodstream form parasites. We transfected parasites with biosensors that measure glucose, ATP, or glycosomal pH. The glucose and ATP sensors were FRET biosensors, while the pH sensor was a GFP-based biosensor. The pH sensor exhibited a different fluorescent profile from the FRET sensors, allowing us to simultaneously measure pH and either glucose or ATP. Cell viability was measured in tandem with the biosensors using thiazole red. We pooled sensor cell lines, loaded them onto plates containing a compound library, and then analyzed them by flow cytometry. The library was analyzed twice, once with the pooled pH and glucose sensor cell lines and once with the pH and ATP sensor cell lines. Multiplexing sensors provided some internal validation of active compounds and gave potential clues for each compound's target(s). We demonstrated this using the glycolytic inhibitor 2-deoxyglucose and the alternative oxidase inhibitor salicylhydroxamic acid. Individual biosensor-based assays exhibited a Z'-factor value acceptable for high-throughput screening, including when multiplexed. We tested assay performance in a pilot screen of 14,976 compounds from the Life Chemicals Compound Library. We obtained hit rates from 0.2 to 0.4% depending on the biosensor, with many compounds impacting multiple sensors. We rescreened 44 hits, and 28 (64%) showed repeatable activity for one or more sensors. One compound exhibited EC50 values in the low micromolar range against two sensors. We expect this method will enable the discovery of glycolytic chemical probes to improve metabolic studies in kinetoplastid parasites.
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Affiliation(s)
- Daniel H Call
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - John Asafo Adjei
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Ryan Pilgrim
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - James W Jeong
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - E Vance Willis
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Ronald A Zegarra
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Nicholas L Tapia
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Madalyn Osterhaus
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Jacob A Vance
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Charles M Voyton
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA; Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - James A Call
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT, USA.
| | - Sabrina S Pizarro
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC, USA.
| | - James C Morris
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC, USA.
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2
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Frei MS, Mehta S, Zhang J. Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism. Annu Rev Biophys 2024; 53:275-297. [PMID: 38346245 DOI: 10.1146/annurev-biophys-030722-021359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of cell signaling and metabolism, as they allow for live-cell measurements with high spatiotemporal resolution. This success has spurred the development of tailor-made biosensors that enable the study of dynamic phenomena on different timescales and length scales. In this review, we discuss different approaches to enhancing and developing new biosensors. We summarize the technologies used to gain structural insights into biosensor design and comment on useful screening technologies. Furthermore, we give an overview of different applications where biosensors have led to key advances over recent years. Finally, we give our perspective on where future work is bound to make a large impact.
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Affiliation(s)
- Michelle S Frei
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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3
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Sakizli U, Takano T, Yoo SK. GALDAR: A genetically encoded galactose sensor for visualizing sugar metabolism in vivo. PLoS Biol 2024; 22:e3002549. [PMID: 38502638 PMCID: PMC10950222 DOI: 10.1371/journal.pbio.3002549] [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: 12/26/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
Sugar metabolism plays a pivotal role in sustaining life. Its dynamics within organisms is less understood compared to its intracellular metabolism. Galactose, a hexose stereoisomer of glucose, is a monosaccharide transported via the same transporters with glucose. Galactose feeds into glycolysis and regulates protein glycosylation. Defects in galactose metabolism are lethal for animals. Here, by transgenically implementing the yeast galactose sensing system into Drosophila, we developed a genetically encoded sensor, GALDAR, which detects galactose in vivo. Using this heterologous system, we revealed dynamics of galactose metabolism in various tissues. Notably, we discovered that intestinal stem cells do not uptake detectable levels of galactose or glucose. GALDAR elucidates the role for galactokinase in metabolism of galactose and a transition of galactose metabolism during the larval period. This work provides a new system that enables analyses of in vivo sugar metabolism.
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Affiliation(s)
- Uğurcan Sakizli
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
| | - Tomomi Takano
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, Japan
| | - Sa Kan Yoo
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, Japan
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4
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Dragic H, Chaveroux C, Cosset E, Manie SN. Modelling cancer metabolism in vitro: current improvements and future challenges. FEBS J 2024; 291:402-411. [PMID: 36516350 DOI: 10.1111/febs.16704] [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: 09/09/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Advances in cancer biology over the past decades have revealed that metabolic adaptation of cancer cells is an essential aspect of tumorigenesis. However, recent insights into tumour metabolism in vivo have revealed dissimilarities with results obtained in vitro. This is partly due to the reductionism of in vitro cancer models that struggle to reproduce the complexity of tumour tissues. This review describes some of the discrepancies in cancer cell metabolism between in vitro and in vivo conditions, and presents current methodological approaches and tools used to bridge the gap with the clinically relevant microenvironment. As such, these approaches should generate new knowledge that could be more effectively translated into therapeutic opportunities.
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Affiliation(s)
- Helena Dragic
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Cedric Chaveroux
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Erika Cosset
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Serge N Manie
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
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5
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Rajkumari N, Chowrasia S, Nishad J, Ganie SA, Mondal TK. Metabolomics-mediated elucidation of rice responses to salt stress. PLANTA 2023; 258:111. [PMID: 37919614 DOI: 10.1007/s00425-023-04258-1] [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: 07/03/2023] [Accepted: 10/01/2023] [Indexed: 11/04/2023]
Abstract
MAIN CONCLUSION Role of salinity responsive metabolites of rice and its wild species has been discussed. Salinity stress is one of the important environmental stresses that severely affects rice productivity. Although, several vital physio-biochemical and molecular responses have been activated in rice under salinity stress which were well described in literatures, the mechanistic role of salt stress and microbes-induced metabolites to overcome salt stress in rice are less studied. Nevertheless, over the years, metabolomic studies have allowed a comprehensive analyses of rice salt stress responses. Hence, we review the salt stress-triggered alterations of various metabolites in rice and discuss their significant roles toward salinity tolerance. Some of the metabolites such as serotonin, salicylic acid, ferulic acid and gentisic acid may act as signaling molecules to activate different downstream salt-tolerance mechanisms; whereas, the other compounds such as amino acids, sugars and organic acids directly act as protective agents to maintain osmotic balance and scavenger of reactive oxygen species during the salinity stress. The quantity, type, tissues specificity and time of accumulation of metabolites induced by salinity stress vary between salt-sensitive and tolerant rice genotypes and thus, contribute to their different degrees of salt tolerance. Moreover, few tolerance metabolites such as allantoin, serotonin and melatonin induce unique pathways for activation of defence mechanisms in salt-tolerant varieties of rice, suggesting their potential roles as the universal biomarkers for salt tolerance. Therefore, these metabolites can be applied exogenously to the sensitive genotypes of rice to enhance their performance under salt stress. Furthermore, the microbes of rhizosphere also participated in rice salt tolerance either directly or indirectly by regulating their metabolic pathways. Thus, this review for the first time offers valuable and comprehensive insights into salt-induced spatio-temporal and genotype-specific metabolites in different genotypes of rice which provide a reference point to analyze stress-gene-metabolite relationships for the biomarker designing in rice. Further, it can also help to decipher several metabolic systems associated with salt tolerance in rice which will be useful in developing salt-tolerance cultivars by conventional breeding/genetic engineering/exogenous application of metabolites.
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Affiliation(s)
- Nitasana Rajkumari
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Soni Chowrasia
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
- Department of Bioscience and Biotechnology, Banastahli Vidyapith, Tonk, Rajasthan, 304022, India
| | - Jyoti Nishad
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India
| | - Showkat Ahmad Ganie
- Plant Molecular Sciences and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, Surrey, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, 110012, India.
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6
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Kim M, Panagiotakopoulou M, Chen C, Ruiz SB, Ganesh K, Tammela T, Heller DA. Micro-engineering and nano-engineering approaches to investigate tumour ecosystems. Nat Rev Cancer 2023; 23:581-599. [PMID: 37353679 PMCID: PMC10528361 DOI: 10.1038/s41568-023-00593-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/25/2023]
Abstract
The interactions among tumour cells, the tumour microenvironment (TME) and non-tumour tissues are of interest to many cancer researchers. Micro-engineering approaches and nanotechnologies are under extensive exploration for modelling these interactions and measuring them in situ and in vivo to investigate therapeutic vulnerabilities in cancer and extend a systemic view of tumour ecosystems. Here we highlight the greatest opportunities for improving the understanding of tumour ecosystems using microfluidic devices, bioprinting or organ-on-a-chip approaches. We also discuss the potential of nanosensors that can transmit information from within the TME or elsewhere in the body to address scientific and clinical questions about changes in chemical gradients, enzymatic activities, metabolic and immune profiles of the TME and circulating analytes. This Review aims to connect the cancer biology and engineering communities, presenting biomedical technologies that may expand the methodologies of the former, while inspiring the latter to develop approaches for interrogating cancer ecosystems.
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Affiliation(s)
- Mijin Kim
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Chen Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Stephen B Ruiz
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Tuomas Tammela
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY, USA
| | - Daniel A Heller
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
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7
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Barros LF, Ruminot I, Sandoval PY, San Martín A. Enlightening brain energy metabolism. Neurobiol Dis 2023:106211. [PMID: 37352985 DOI: 10.1016/j.nbd.2023.106211] [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: 03/06/2023] [Revised: 05/06/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Brain tissue metabolism is distributed across several cell types and subcellular compartments, which activate at different times and with different temporal patterns. The introduction of genetically-encoded fluorescent indicators that are imaged using time-lapse microscopy has opened the possibility of studying brain metabolism at cellular and sub-cellular levels. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides, which inform about relative levels, concentrations and fluxes. This review offers a brief survey of the metabolic indicators that have been validated in brain cells, with some illustrative examples from the literature. Whereas only a small fraction of the metabolome is currently accessible to fluorescent probes, there are grounds to be optimistic about coming developments and the application of these tools to the study of brain disease.
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Affiliation(s)
- L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile.
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Ciencias para el Cuidado de La Salud, Universidad San Sebastián, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Ciencias para el Cuidado de La Salud, Universidad San Sebastián, Valdivia, Chile
| | - A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Ciencias para el Cuidado de La Salud, Universidad San Sebastián, Valdivia, Chile
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8
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Murugappan K, Sundaramoorthy U, Damry AM, Nisbet DR, Jackson CJ, Tricoli A. Electrodetection of Small Molecules by Conformation-Mediated Signal Enhancement. JACS AU 2022; 2:2481-2490. [PMID: 36465535 PMCID: PMC9709943 DOI: 10.1021/jacsau.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 06/17/2023]
Abstract
Electrochemical biosensors allow the rapid, selective, and sensitive transduction of critical biological parameters into measurable signals. However, current electrochemical biosensors often fail to selectively and sensitively detect small molecules because of their small size and low molecular complexity. We have developed an electrochemical biosensing platform that harnesses the analyte-dependent conformational change of highly selective solute-binding proteins to amplify the redox signal generated by analyte binding. Using this platform, we constructed and characterized two biosensors that can sense leucine and glycine, respectively. We show that these biosensors can selectively and sensitively detect their targets over a wide range of concentrations-up to 7 orders of magnitude-and that the selectivity of these sensors can be readily altered by switching the bioreceptor's binding domain. Our work represents a new paradigm for the design of a family of modular electrochemical biosensors, where access to electrode surfaces can be controlled by protein conformational changes.
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Affiliation(s)
- Krishnan Murugappan
- Nanotechnology
Research Laboratory, Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT2601, Australia
- CSIRO,
Mineral Resources, Private
Bag 10, Clayton South, VIC3169, Australia
| | | | - Adam M. Damry
- Research
School of Chemistry, The Australian National
University, Canberra, ACT2601, Australia
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ONK1N 6N5, Canada
| | - David R. Nisbet
- Laboratory
of Advanced Biomaterials, Research School of Chemistry and the John
Curtin School of Medical Research, The Australian
National University, Canberra, ACT2601, Australia
- The Graeme
Clark Institute, The University of Melbourne, Melbourne, VIC3010, Australia
- Department
of Biomedical Engineering, Faculty of Engineering and Information
Technology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, The Australian National
University, Canberra, ACT2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, The Australian National University, Canberra, ACT2601, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, The Australian National
University, Canberra, ACT2601, Australia
| | - Antonio Tricoli
- Nanotechnology
Research Laboratory, Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT2601, Australia
- Nanotechnology
Research Laboratory, Faculty of Engineering, University of Sydney, Sydney, NSW2006, Australia
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9
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Jiang H, Kimura T, Hai H, Yamamura R, Sonoshita M. Drosophila as a toolkit to tackle cancer and its metabolism. Front Oncol 2022; 12:982751. [PMID: 36091180 PMCID: PMC9458318 DOI: 10.3389/fonc.2022.982751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer is one of the most severe health problems worldwide accounting for the second leading cause of death. Studies have indicated that cancers utilize different metabolic systems as compared with normal cells to produce extra energy and substances required for their survival, which contributes to tumor formation and progression. Recently, the fruit fly Drosophila has been attracting significant attention as a whole-body model for elucidating the cancer mechanisms including metabolism. This tiny organism offers a valuable toolkit with various advantages such as high genetic conservation and similar drug response to mammals. In this review, we introduce flies modeling for cancer patient genotypes which have pinpointed novel therapeutic targets and drug candidates in the salivary gland, thyroid, colon, lung, and brain. Furthermore, we introduce fly models for metabolic diseases such as diabetes mellitus, obesity, and cachexia. Diabetes mellitus and obesity are widely acknowledged risk factors for cancer, while cachexia is a cancer-related metabolic condition. In addition, we specifically focus on two cancer metabolic alterations: the Warburg effect and redox metabolism. Indeed, flies proved useful to reveal the relationship between these metabolic changes and cancer. Such accumulating achievements indicate that Drosophila offers an efficient platform to clarify the mechanisms of cancer as a systemic disease.
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Affiliation(s)
- Hui Jiang
- Division of Biomedical Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Taku Kimura
- Division of Biomedical Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Department of Oral Diagnosis and Medicine, Graduate school of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Han Hai
- Division of Biomedical Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Ryodai Yamamura
- Division of Biomedical Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- *Correspondence: Ryodai Yamamura, ; Masahiro Sonoshita,
| | - Masahiro Sonoshita
- Division of Biomedical Oncology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- *Correspondence: Ryodai Yamamura, ; Masahiro Sonoshita,
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2-deoxyglucose transiently inhibits yeast AMPK signaling and triggers glucose transporter endocytosis, potentiating the drug toxicity. PLoS Genet 2022; 18:e1010169. [PMID: 35951639 PMCID: PMC9398028 DOI: 10.1371/journal.pgen.1010169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/23/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
2-deoxyglucose is a glucose analog that impacts many aspects of cellular physiology. After its uptake and its phosphorylation into 2-deoxyglucose-6-phosphate (2DG6P), it interferes with several metabolic pathways including glycolysis and protein N-glycosylation. Despite this systemic effect, resistance can arise through strategies that are only partially understood. In yeast, 2DG resistance is often associated with mutations causing increased activity of the yeast 5’-AMP activated protein kinase (AMPK), Snf1. Here we focus on the contribution of a Snf1 substrate in 2DG resistance, namely the alpha-arrestin Rod1 involved in nutrient transporter endocytosis. We report that 2DG triggers the endocytosis of many plasma membrane proteins, mostly in a Rod1-dependent manner. Rod1 participates in 2DG-induced endocytosis because 2DG, following its phosphorylation by hexokinase Hxk2, triggers changes in Rod1 post-translational modifications and promotes its function in endocytosis. Mechanistically, this is explained by a transient, 2DG-induced inactivation of Snf1/AMPK by protein phosphatase 1 (PP1). We show that 2DG-induced endocytosis is detrimental to cells, and the lack of Rod1 counteracts this process by stabilizing glucose transporters at the plasma membrane. This facilitates glucose uptake, which may help override the metabolic blockade caused by 2DG, and 2DG export—thus terminating the process of 2DG detoxification. Altogether, these results shed a new light on the regulation of AMPK signaling in yeast and highlight a remarkable strategy to bypass 2DG toxicity involving glucose transporter regulation.
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Hirrlinger J, Nimmerjahn A. A perspective on astrocyte regulation of neural circuit function and animal behavior. Glia 2022; 70:1554-1580. [PMID: 35297525 PMCID: PMC9291267 DOI: 10.1002/glia.24168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/19/2022] [Accepted: 02/27/2022] [Indexed: 12/16/2022]
Abstract
Studies over the past two decades have demonstrated that astrocytes are tightly associated with neurons and play pivotal roles in neural circuit development, operation, and adaptation in health and disease. Nevertheless, precisely how astrocytes integrate diverse neuronal signals, modulate neural circuit structure and function at multiple temporal and spatial scales, and influence animal behavior or disease through aberrant excitation and molecular output remains unclear. This Perspective discusses how new and state-of-the-art approaches, including fluorescence indicators, opto- and chemogenetic actuators, genetic targeting tools, quantitative behavioral assays, and computational methods, might help resolve these longstanding questions. It also addresses complicating factors in interpreting astrocytes' role in neural circuit regulation and animal behavior, such as their heterogeneity, metabolism, and inter-glial communication. Research on these questions should provide a deeper mechanistic understanding of astrocyte-neuron assemblies' role in neural circuit function, complex behaviors, and disease.
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Affiliation(s)
- Johannes Hirrlinger
- Carl-Ludwig-Institute for Physiology, Medical Faculty,
University of Leipzig, Leipzig, Germany
- Department of Neurogenetics, Max-Planck-Institute for
Multidisciplinary Sciences, Göttingen, Germany
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, The Salk Institute for
Biological Studies, La Jolla, California
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12
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Kim H, Choi G, Suk ME, Kim TJ. Resource for FRET-Based Biosensor Optimization. Front Cell Dev Biol 2022; 10:885394. [PMID: 35794864 PMCID: PMC9251444 DOI: 10.3389/fcell.2022.885394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
After the development of Cameleon, the first fluorescence resonance energy transfer (FRET)-based calcium indicator, a variety of FRET-based genetically encoded biosensors (GEBs) have visualized numerous target players to monitor their cell physiological dynamics spatiotemporally. Many attempts have been made to optimize GEBs, which require labor-intensive effort, novel approaches, and precedents to develop more sensitive and versatile biosensors. However, researchers face considerable trial and error in upgrading biosensors because examples and methods of improving FRET-based GEBs are not well documented. In this review, we organize various optimization strategies after assembling the existing cases in which the non-fluorescent components of biosensors are upgraded. In addition, promising areas to which optimized biosensors can be applied are briefly discussed. Therefore, this review could serve as a resource for researchers attempting FRET-based GEB optimization.
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Affiliation(s)
- Heonsu Kim
- Institute of Systems Biology, Pusan National University, Busan, South Korea
| | - Gyuho Choi
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Myung Eun Suk
- Department of Mechanical Engineering, IT Convergence College of Materials and Components Engineering, Dong-Eui University, Busan, South Korea
- *Correspondence: Myung Eun Suk, ; Tae-Jin Kim,
| | - Tae-Jin Kim
- Institute of Systems Biology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Biological Sciences, Pusan National University, Busan, South Korea
- *Correspondence: Myung Eun Suk, ; Tae-Jin Kim,
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Sargazi S, Fatima I, Hassan Kiani M, Mohammadzadeh V, Arshad R, Bilal M, Rahdar A, Díez-Pascual AM, Behzadmehr R. Fluorescent-based nanosensors for selective detection of a wide range of biological macromolecules: A comprehensive review. Int J Biol Macromol 2022; 206:115-147. [PMID: 35231532 DOI: 10.1016/j.ijbiomac.2022.02.137] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
Abstract
Thanks to their unique attributes, such as good sensitivity, selectivity, high surface-to-volume ratio, and versatile optical and electronic properties, fluorescent-based bioprobes have been used to create highly sensitive nanobiosensors to detect various biological and chemical agents. These sensors are superior to other analytical instrumentation techniques like gas chromatography, high-performance liquid chromatography, and capillary electrophoresis for being biodegradable, eco-friendly, and more economical, operational, and cost-effective. Moreover, several reports have also highlighted their application in the early detection of biomarkers associated with drug-induced organ damage such as liver, kidney, or lungs. In the present work, we comprehensively overviewed the electrochemical sensors that employ nanomaterials (nanoparticles/colloids or quantum dots, carbon dots, or nanoscaled metal-organic frameworks, etc.) to detect a variety of biological macromolecules based on fluorescent emission spectra. In addition, the most important mechanisms and methods to sense amino acids, protein, peptides, enzymes, carbohydrates, neurotransmitters, nucleic acids, vitamins, ions, metals, and electrolytes, blood gases, drugs (i.e., anti-inflammatory agents and antibiotics), toxins, alkaloids, antioxidants, cancer biomarkers, urinary metabolites (i.e., urea, uric acid, and creatinine), and pathogenic microorganisms were outlined and compared in terms of their selectivity and sensitivity. Altogether, the small dimensions and capability of these nanosensors for sensitive, label-free, real-time sensing of chemical, biological, and pharmaceutical agents could be used in array-based screening and in-vitro or in-vivo diagnostics. Although fluorescent nanoprobes are widely applied in determining biological macromolecules, unfortunately, they present many challenges and limitations. Efforts must be made to minimize such limitations in utilizing such nanobiosensors with an emphasis on their commercial developments. We believe that the current review can foster the wider incorporation of nanomedicine and will be of particular interest to researchers working on fluorescence technology, material chemistry, coordination polymers, and related research areas.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, 98167-43463 Zahedan, Iran
| | - Iqra Fatima
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Maria Hassan Kiani
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Vahideh Mohammadzadeh
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Science, Mashhad 1313199137, Iran
| | - Rabia Arshad
- Faculty of Pharmacy, University of Lahore, Lahore 45320, Pakistan
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, P. O. Box. 98613-35856, Iran.
| | - Ana M Díez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona, Km. 33.6, 28805 Alcalá de Henares, Madrid, Spain.
| | - Razieh Behzadmehr
- Department of Radiology, Zabol University of Medical Sciences, Zabol, Iran
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14
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San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
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Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
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15
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Allert MJ, Hellinga HW. Discovery of Thermostable, Fluorescently Responsive Glucose Biosensors by Structure-Assisted Function Extrapolation. Biochemistry 2022; 61:276-293. [PMID: 35084821 DOI: 10.1021/acs.biochem.1c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate assignment of protein function from sequence remains a fascinating and difficult challenge. The periplasmic-binding protein (PBP) superfamily present an interesting case of function prediction because they are both ubiquitous in prokaryotes and tend to diversify through gene duplication "explosions" that can lead to large numbers of paralogs in a genome. An engineered version of the moderately thermostable glucose-binding PBP from Escherichia coli has been used successfully as a reagentless fluorescent biosensor both in vitro and in vivo. To develop more robust sensors that meet the challenges of real-world applications, we report the discovery of thermostable homologues that retain a glucose-mediated conformationally coupled fluorescence response. Accurately identifying a glucose-binding PBP homologue among closely related paralogs is challenging. We demonstrate that a structure-based method that filters sequences by residues that bind glucose in an archetype structure is highly effective. Using fully sequenced bacterial genomes, we found that this filter reduced high paralog numbers to single hits in a genome, consistent with the accurate separation of glucose binding from other functions. We expressed engineered proteins for eight homologues, chosen to represent different degrees of sequence identity, and tested their glucose-mediated fluorescence responses. We accurately predicted the presence of glucose binding down to 31% sequence identity. We have also successfully identified suitable candidates for next-generation robust, fluorescent glucose sensors.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
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16
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Chandris P, Giannouli CC, Panayotou G. Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters. Front Cell Dev Biol 2022; 9:725114. [PMID: 35118062 PMCID: PMC8804523 DOI: 10.3389/fcell.2021.725114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of "watching metabolism in real time."
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Affiliation(s)
- Panagiotis Chandris
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
| | | | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
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17
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McMullen E, Hertenstein H, Müller S, Schirmeier S. Genetically Encoded Sensors to Study Metabolism in Drosophila. Methods Mol Biol 2022; 2540:401-414. [PMID: 35980591 DOI: 10.1007/978-1-0716-2541-5_21] [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: 06/15/2023]
Abstract
The rather recent development of genetically encoded metabolite sensors has changed the way we can study metabolism in living cells, ex vivo tissues, and in vivo immensely. In recent years, these sensors have also been adapted for use in Drosophila tissues. Here, we describe a standard protocol to image such sensors in ex vivo Drosophila larval brains using the glucose sensor FLII12Pglu-700μδ6. The protocol, however, can be adapted for the use of other sensors, tissues, and can even be used in vivo.
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Affiliation(s)
- Ellen McMullen
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Helen Hertenstein
- Department of Biology, Institute of Zoology, Technische Universität Dresden, Dresden, Germany
| | - Stephan Müller
- Department of Biology, Institute of Zoology, Technische Universität Dresden, Dresden, Germany
| | - Stefanie Schirmeier
- Department of Biology, Institute of Zoology, Technische Universität Dresden, Dresden, Germany.
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18
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Bekdash R, Quejada JR, Ueno S, Kawano F, Morikawa K, Klein AD, Matsumoto K, Lee TC, Nakanishi K, Chalan A, Lee TM, Liu R, Homma S, Lin CS, Yelshanskaya MV, Sobolevsky AI, Goda K, Yazawa M. GEM-IL: A highly responsive fluorescent lactate indicator. CELL REPORTS METHODS 2021; 1:100092. [PMID: 35475001 PMCID: PMC9017230 DOI: 10.1016/j.crmeth.2021.100092] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 07/26/2021] [Accepted: 09/15/2021] [Indexed: 12/22/2022]
Abstract
Lactate metabolism has been shown to have increasingly important implications in cellular functions as well as in the development and pathophysiology of disease. The various roles as a signaling molecule and metabolite have led to interest in establishing a new method to detect lactate changes in live cells. Here we report our development of a genetically encoded metabolic indicator specifically for probing lactate (GEM-IL) based on superfolder fluorescent proteins and mutagenesis. With improvements in its design, specificity, and sensitivity, GEM-IL allows new applications compared with the previous lactate indicators, Laconic and Green Lindoblum. We demonstrate the functionality of GEM-IL to detect differences in lactate changes in human oncogenic neural progenitor cells and mouse primary ventricular myocytes. The development and application of GEM-IL show promise for enhancing our understanding of lactate dynamics and roles.
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Affiliation(s)
- Ramsey Bekdash
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jose R. Quejada
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Shunnosuke Ueno
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Fuun Kawano
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
| | - Kumi Morikawa
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
| | - Alison D. Klein
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
| | - Kenji Matsumoto
- Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Tetz C. Lee
- Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Koki Nakanishi
- Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Amy Chalan
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
| | - Teresa M. Lee
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Rui Liu
- Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Shunichi Homma
- Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Chyuan-Sheng Lin
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Transgenic Mouse Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Maria V. Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Alexander I. Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- Institute of Technological Sciences, Wuhan University, Hubei 430072, China
| | - Masayuki Yazawa
- Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
- Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, 650 West 168th Street, BB1108/BB1109D, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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19
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Sadoine M, Ishikawa Y, Kleist TJ, Wudick MM, Nakamura M, Grossmann G, Frommer WB, Ho CH. Designs, applications, and limitations of genetically encoded fluorescent sensors to explore plant biology. PLANT PHYSIOLOGY 2021; 187:485-503. [PMID: 35237822 PMCID: PMC8491070 DOI: 10.1093/plphys/kiab353] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/12/2021] [Indexed: 05/03/2023]
Abstract
The understanding of signaling and metabolic processes in multicellular organisms requires knowledge of the spatial dynamics of small molecules and the activities of enzymes, transporters, and other proteins in vivo, as well as biophysical parameters inside cells and across tissues. The cellular distribution of receptors, ligands, and activation state must be integrated with information about the cellular distribution of metabolites in relation to metabolic fluxes and signaling dynamics in order to achieve the promise of in vivo biochemistry. Genetically encoded sensors are engineered fluorescent proteins that have been developed for a wide range of small molecules, such as ions and metabolites, or to report biophysical processes, such as transmembrane voltage or tension. First steps have been taken to monitor the activity of transporters in vivo. Advancements in imaging technologies and specimen handling and stimulation have enabled researchers in plant sciences to implement sensor technologies in intact plants. Here, we provide a brief history of the development of genetically encoded sensors and an overview of the types of sensors available for quantifying and visualizing ion and metabolite distribution and dynamics. We further discuss the pros and cons of specific sensor designs, imaging systems, and sample manipulations, provide advice on the choice of technology, and give an outlook into future developments.
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Affiliation(s)
- Mayuri Sadoine
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Yuuma Ishikawa
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Thomas J. Kleist
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Michael M. Wudick
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Guido Grossmann
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute for Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B. Frommer
- Molecular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Cheng-Hsun Ho
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Author for communication:
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20
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Bonvento G, Bolaños JP. Astrocyte-neuron metabolic cooperation shapes brain activity. Cell Metab 2021; 33:1546-1564. [PMID: 34348099 DOI: 10.1016/j.cmet.2021.07.006] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/11/2021] [Accepted: 07/03/2021] [Indexed: 12/12/2022]
Abstract
The brain has almost no energy reserve, but its activity coordinates organismal function, a burden that requires precise coupling between neurotransmission and energy metabolism. Deciphering how the brain accomplishes this complex task is crucial to understand central facets of human physiology and disease mechanisms. Each type of neural cell displays a peculiar metabolic signature, forcing the intercellular exchange of metabolites that serve as both energy precursors and paracrine signals. The paradigm of this biological feature is the astrocyte-neuron couple, in which the glycolytic metabolism of astrocytes contrasts with the mitochondrial oxidative activity of neurons. Astrocytes generate abundant mitochondrial reactive oxygen species and shuttle to neurons glycolytically derived metabolites, such as L-lactate and L-serine, which sustain energy needs, conserve redox status, and modulate neurotransmitter-receptor activity. Conversely, early disruption of this metabolic cooperation may contribute to the initiation or progression of several neurological diseases, thus requiring innovative therapies to preserve brain energetics.
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Affiliation(s)
- Gilles Bonvento
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France.
| | - Juan P Bolaños
- Institute of Functional Biology and Genomics (IBFG), Universidad de Salamanca, CSIC, Salamanca, Spain; Centro de Investigación Biomédica en Red sobre Fragilidad y Envejecimiento Saludable (CIBERFES), Institute of Biomedical Research of Salamanca, Salamanca, Spain
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21
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Garagounis C, Delkis N, Papadopoulou KK. Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors. THE NEW PHYTOLOGIST 2021; 231:1338-1352. [PMID: 33997999 DOI: 10.1111/nph.17470] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 05/25/2023]
Abstract
Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.
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Affiliation(s)
- Constantine Garagounis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Nikolaos Delkis
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Plant and Environmental Biotechnology Laboratory, University of Thessaly, Larissa, 41500, Greece
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22
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Chang TJ, Lai WQ, Chang YF, Wang CL, Yang DM. Development and optimization of heavy metal lead biosensors in biomedical and environmental applications. J Chin Med Assoc 2021; 84:745-753. [PMID: 34225337 DOI: 10.1097/jcma.0000000000000574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The detrimental impact of the heavy metal lead (Pb) on human health has been studied for years. The fact that Pb impairs human body has been established from countless painful and sad historical events. Nowadays, World Health Organization and many developmental countries have established regulations concerning the use of Pb. Measuring the blood lead level (BLL) is so far the only way to officially evaluate the degree of Pb exposure, but the so-called safety value (10 μg/dL in adults and 5 μg/dL in children) seems unreliable to represent the security checkpoint for children through daily intake of drinking water or physical contact with a lower contaminated level of Pb contents. In general, unsolved mysteries about the Pb toxicological mechanisms still remain. In this review article, we report on the methods to prevent Pb poison for further Pb toxicological research. We establish high-sensitivity Pb monitoring, and also report on the use of fluorescent biosensors such as genetically-encoded fluorescence resonance energy transfer-based biosensors built for various large demands such as the detection of severe acute respiratory syndrome coronavirus 2. We also contribute to the development and optimization of the FRET-based Pb biosensors. Our well-performed version of Met-lead 1.44 M1 has achieved a limit of detection of 10 nM (2 ppb; 0.2 μg/dL) and almost 5-fold in dynamic range (DR) supported for the real practical applications-that is, the in-cell Pb sensing device for blood and blood-related samples, and the Pb environmental detections in vitro. The perspective of our powerful Pb biosensor incorporated with a highly sensitive bio-chip of the portable device for quick Pb measurements will be addressed for further manipulation.
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Affiliation(s)
- Tai-Jay Chang
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Wei-Qun Lai
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yu-Fen Chang
- LumiSTAR Biotechnology, Inc., Taipei, Taiwan, ROC
| | - Chia-Lin Wang
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - De-Ming Yang
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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23
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Mita M, Sugawara I, Harada K, Ito M, Takizawa M, Ishida K, Ueda H, Kitaguchi T, Tsuboi T. Development of red genetically encoded biosensor for visualization of intracellular glucose dynamics. Cell Chem Biol 2021; 29:98-108.e4. [PMID: 34197723 DOI: 10.1016/j.chembiol.2021.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Glucose is the main source of energy for organisms, and it is important to understand the spatiotemporal dynamics of intracellular glucose. Single fluorescent protein-based glucose indicators, named "Red Glifons" have been developed that apply to live-cell and dual-color imaging. These indicators exhibited more than 3-fold increase in fluorescence intensity in the presence of 10 mM glucose. The two Red Glifons developed have different half-maximal effective concentration (EC50) values for glucose (300 μM and 3,000 μM) and are able to monitor a wide range of glucose dynamics. Red Glifon combined with green indicators allowing visualization of the interplay between glucose and ATP, lactate, or pyruvate. Glucose influx in the pharyngeal muscle of Caenorhabditis elegans, enteroendocrine cells, and human iPS cell-derived cardiac myocytes was observed using the Red Glifons. Thus these red glucose indicators serve as a multi-color imaging toolkit for investigating complex interactions in energy metabolism.
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Affiliation(s)
- Marie Mita
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Izumi Sugawara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Kazuki Harada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Motoki Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Mai Takizawa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kentaro Ishida
- Myoridge Co. Ltd., 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
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24
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Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL. In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor. Cell Rep 2021; 35:109284. [PMID: 34161775 DOI: 10.1016/j.celrep.2021.109284] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 03/06/2020] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Glucose is arguably the most important molecule in metabolism, and its dysregulation underlies diabetes. We describe a family of single-wavelength genetically encoded glucose sensors with a high signal-to-noise ratio, fast kinetics, and affinities varying over four orders of magnitude (1 μM to 10 mM). The sensors allow mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed ∼3-fold faster glucose changes in astrocytes. In larval Drosophila central nervous system explants, intracellular neuronal glucose fluxes suggested a rostro-caudal transport pathway in the ventral nerve cord neuropil. In zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory and pharmacological perturbations produced large changes in the brain. These sensors will enable rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.
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Affiliation(s)
- Jacob P Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Haluk Lacin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - William C Lemon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Soomin Kim
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Richard T Lee
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA; The Cardiovascular Division, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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25
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Murphy KJ, Reed DA, Trpceski M, Herrmann D, Timpson P. Quantifying and visualising the nuances of cellular dynamics in vivo using intravital imaging. Curr Opin Cell Biol 2021; 72:41-53. [PMID: 34091131 DOI: 10.1016/j.ceb.2021.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022]
Abstract
Intravital imaging is a powerful technology used to quantify and track dynamic changes in live cells and tissues within an intact environment. The ability to watch cell biology in real-time 'as it happens' has provided novel insight into tissue homeostasis, as well as disease initiation, progression and response to treatment. In this minireview, we highlight recent advances in the field of intravital microscopy, touching upon advances in awake versus anaesthesia-based approaches, as well as the integration of biosensors into intravital imaging. We also discuss current challenges that, in our opinion, need to be overcome to further advance the field of intravital imaging at the single-cell, subcellular and molecular resolution to reveal nuances of cell behaviour that can be targeted in complex disease settings.
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Affiliation(s)
- Kendelle J Murphy
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Daniel A Reed
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Michael Trpceski
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia
| | - David Herrmann
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia.
| | - Paul Timpson
- Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Cancer Theme, Sydney, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2010, Australia.
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26
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Sadoine M, Reger M, Wong KM, Frommer WB. Affinity Series of Genetically Encoded Förster Resonance Energy-Transfer Sensors for Sucrose. ACS Sens 2021; 6:1779-1784. [PMID: 33974799 DOI: 10.1021/acssensors.0c02495] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genetically encoded fluorescent sugar sensors are valuable tools for the discovery of transporters and for quantitative monitoring of sugar steady-state levels in intact tissues. Genetically encoded Förster resonance energy-transfer sensors for glucose have been designed and optimized extensively, and a full series of affinity mutants is available for in vivo studies. However, to date, only a single improved sucrose sensor FLIPsuc-90μΔ1 with Km for sucrose of ∼90 μM was available. This sucrose sensor was engineered on the basis of an Agrobacterium tumefaciens sugar-binding protein. Here, we took a two-step approach to first improve the dynamic range of the FLIPsuc sensor and then expand the detection range from micro- to millimolar sucrose concentrations by mutating a key residue in the binding site. The resulting series of sucrose sensors may enable investigation of sucrose transporter candidates and comprehensive in vivo analyses of sucrose concentration in plants. Since FLIPsuc-90μ also detects trehalose in animal cells, the new series of sensors will likely be suitable for investigating trehalose transport and monitor trehalose steady-state levels in vivo.
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Affiliation(s)
- Mayuri Sadoine
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Mira Reger
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, United States
| | - Ka Man Wong
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, United States
| | - Wolf B. Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, United States
- Institute for Transformative Biomolecules, ITbM, Nagoya University, Nagoya, Aichi 464-8601, Japan
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27
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Hong S, Pawel GT, Pei R, Lu Y. Recent progress in developing fluorescent probes for imaging cell metabolites. Biomed Mater 2021; 16. [PMID: 33915523 DOI: 10.1088/1748-605x/abfd11] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/29/2021] [Indexed: 01/12/2023]
Abstract
Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.
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Affiliation(s)
- Shanni Hong
- Department of Medical Imaging Technology, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.,CAS Key Laboratory of Nano-Bio Interfaces, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, People's Republic of China
| | - Gregory T Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interfaces, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, People's Republic of China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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28
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Wang C, Xia C, Zhu Y, Zhang H. Innovative fluorescent probes for in vivo visualization of biomolecules in living Caenorhabditis elegans. Cytometry A 2021; 99:560-574. [PMID: 33638604 DOI: 10.1002/cyto.a.24325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Caenorhabditis elegans (C. elegans) as a well-established multicellular model organism has been widely used in the biological field for half a century. Its numerous advantages including small body size, rapid life cycle, high-reproductive rate, well-defined anatomy, and conserved genome, has made C. elegans one of the most successful multicellular model organisms. Discoveries obtained from the C. elegans model have made great contributions to research fields such as development, aging, biophysics, immunology, and neuroscience. Because of its transparent body and giant cell size, C. elegans is also an ideal subject for high resolution and high-throughput optical imaging and analysis. During the past decade, great advances have been made to develop biomolecule-targeting techniques for noninvasive optical imaging. These novel technologies expanded the toolbox for qualitative and quantitative analysis of biomolecules in C. elegans. In this review, we summarize recently developed fluorescent probes or labeling techniques for visualizing biomolecules at the cellular, subcellular or molecular scale by using C. elegans as the major model organism or designed specifically for the applications in C. elegans. Combining the technological advantages of the C. elegans model with the novel fluorescent labeling techniques will provide new horizons for high-efficiency quantitative optical analysis in live organisms.
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Affiliation(s)
- Chunxia Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chujie Xia
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yi Zhu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Huimin Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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29
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Horvat A, Muhič M, Smolič T, Begić E, Zorec R, Kreft M, Vardjan N. Ca 2+ as the prime trigger of aerobic glycolysis in astrocytes. Cell Calcium 2021; 95:102368. [PMID: 33621899 DOI: 10.1016/j.ceca.2021.102368] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/17/2022]
Abstract
Astroglial aerobic glycolysis, a process during which d-glucose is converted to l-lactate, a brain fuel and signal, is regulated by the plasmalemmal receptors, including adrenergic receptors (ARs) and purinergic receptors (PRs), modulating intracellular Ca2+ and cAMP signals. However, the extent to which the two signals regulate astroglial aerobic glycolysis is poorly understood. By using agonists to stimulate intracellular α1-/β-AR-mediated Ca2+/cAMP signals, β-AR-mediated cAMP and P2R-mediated Ca2+ signals and genetically encoded fluorescence resonance energy transfer-based glucose and lactate nanosensors in combination with real-time microscopy, we show that intracellular Ca2+, but not cAMP, initiates a robust increase in the concentration of intracellular free d-glucose ([glc]i) and l-lactate ([lac]i), both depending on extracellular d-glucose, suggesting Ca2+-triggered glucose uptake and aerobic glycolysis in astrocytes. When the glycogen shunt, a process of glycogen remodelling, was inhibited, the α1-/β-AR-mediated increases in [glc]i and [lac]i were reduced by ∼65 % and ∼30 %, respectively, indicating that at least ∼30 % of the utilization of d-glucose is linked to glycogen remodelling and aerobic glycolysis. Additional activation of β-AR/cAMP signals aided to α1-/β-AR-triggered [lac]i increase, whereas the [glc]i increase was unaltered. Taken together, an increase in intracellular Ca2+ is the prime mechanism of augmented aerobic glycolysis in astrocytes, while cAMP has only a moderate role. The results provide novel information on the signals regulating brain metabolism and open new avenues to explore whether astroglial Ca2+ signals are dysregulated and contribute to neuropathologies with impaired brain metabolism.
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Affiliation(s)
- Anemari Horvat
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia
| | - Marko Muhič
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tina Smolič
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ena Begić
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Robert Zorec
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia
| | - Marko Kreft
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia; Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Vardjan
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia.
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30
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McMullen E, Weiler A, Becker HM, Schirmeier S. Plasticity of Carbohydrate Transport at the Blood-Brain Barrier. Front Behav Neurosci 2021; 14:612430. [PMID: 33551766 PMCID: PMC7863721 DOI: 10.3389/fnbeh.2020.612430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/17/2020] [Indexed: 12/21/2022] Open
Abstract
Neuronal function is highly energy demanding, requiring efficient transport of nutrients into the central nervous system (CNS). Simultaneously the brain must be protected from the influx of unwanted solutes. Most of the energy is supplied from dietary sugars, delivered from circulation via the blood-brain barrier (BBB). Therefore, selective transporters are required to shuttle metabolites into the nervous system where they can be utilized. The Drosophila BBB is formed by perineural and subperineurial glial cells, which effectively separate the brain from the surrounding hemolymph, maintaining a constant microenvironment. We identified two previously unknown BBB transporters, MFS3 (Major Facilitator Superfamily Transporter 3), located in the perineurial glial cells, and Pippin, found in both the perineurial and subperineurial glial cells. Both transporters facilitate uptake of circulating trehalose and glucose into the BBB-forming glial cells. RNA interference-mediated knockdown of these transporters leads to pupal lethality. However, null mutants reach adulthood, although they do show reduced lifespan and activity. Here, we report that both carbohydrate transport efficiency and resulting lethality found upon loss of MFS3 or Pippin are rescued via compensatory upregulation of Tret1-1, another BBB carbohydrate transporter, in Mfs3 and pippin null mutants, while RNAi-mediated knockdown is not compensated for. This means that the compensatory mechanisms in place upon mRNA degradation following RNA interference can be vastly different from those resulting from a null mutation.
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Affiliation(s)
- Ellen McMullen
- Department of Biology, Institute of Zoology, Technische Universität Dresden, Dresden, Germany
| | - Astrid Weiler
- Department of Biology, Institute of Zoology, Technische Universität Dresden, Dresden, Germany
| | - Holger M. Becker
- Division of General Zoology, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Stefanie Schirmeier
- Department of Biology, Institute of Zoology, Technische Universität Dresden, Dresden, Germany
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31
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Isoda R, Yoshinari A, Ishikawa Y, Sadoine M, Simon R, Frommer WB, Nakamura M. Sensors for the quantification, localization and analysis of the dynamics of plant hormones. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:542-557. [PMID: 33231903 PMCID: PMC7898640 DOI: 10.1111/tpj.15096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/19/2020] [Indexed: 05/13/2023]
Abstract
Plant hormones play important roles in plant growth and development and physiology, and in acclimation to environmental changes. The hormone signaling networks are highly complex and interconnected. It is thus important to not only know where the hormones are produced, how they are transported and how and where they are perceived, but also to monitor their distribution quantitatively, ideally in a non-invasive manner. Here we summarize the diverse set of tools available for quantifying and visualizing hormone distribution and dynamics. We provide an overview over the tools that are currently available, including transcriptional reporters, degradation sensors, and luciferase and fluorescent sensors, and compare the tools and their suitability for different purposes.
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Affiliation(s)
- Reika Isoda
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Akira Yoshinari
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Yuuma Ishikawa
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Mayuri Sadoine
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Rüdiger Simon
- Developmental GeneticsHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Wolf B. Frommer
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Masayoshi Nakamura
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
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32
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Fernández-Moncada I, Robles-Maldonado D, Castro P, Alegría K, Epp R, Ruminot I, Barros LF. Bidirectional astrocytic GLUT1 activation by elevated extracellular K . Glia 2020; 69:1012-1021. [PMID: 33277953 DOI: 10.1002/glia.23944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/07/2023]
Abstract
The acute rise in interstitial K+ that accompanies neural activity couples the energy demand of neurons to the metabolism of astrocytes. The effects of elevated K+ on astrocytes include activation of aerobic glycolysis, inhibition of mitochondrial respiration and the release of lactate. Using a genetically encoded FRET glucose sensor and a novel protocol based on 3-O-methylglucose trans-acceleration and numerical simulation of glucose dynamics, we report that extracellular K+ is also a potent and reversible modulator of the astrocytic glucose transporter GLUT1. In cultured mouse astrocytes, the stimulatory effect developed within seconds, engaged both the influx and efflux modes of the transporter, and was detected even at 1 mM incremental K+ . The modulation of GLUT1 explains how astrocytes are able to maintain their glucose pool in the face of strong glycolysis stimulation. We propose that the stimulation of GLUT1 by K+ supports the production of lactate by astrocytes and the timely delivery of glucose to active neurons.
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Affiliation(s)
- Ignacio Fernández-Moncada
- Centro de Estudios Científicos, Valdivia, Chile.,INSERM U1215 NeuroCentre Magendie, Bordeaux, France
| | - Daniel Robles-Maldonado
- Centro de Estudios Científicos, Valdivia, Chile.,Universidad Austral de Chile, Valdivia, Chile
| | | | | | - Robert Epp
- Institute of Fluid Dynamics, ETH Zurich, Zurich, Switzerland
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33
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Köhler S, Schmidt H, Fülle P, Hirrlinger J, Winkler U. A Dual Nanosensor Approach to Determine the Cytosolic Concentration of ATP in Astrocytes. Front Cell Neurosci 2020; 14:565921. [PMID: 33192312 PMCID: PMC7530325 DOI: 10.3389/fncel.2020.565921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/26/2020] [Indexed: 11/17/2022] Open
Abstract
Adenosine triphosphate (ATP) is the central energy carrier of all cells and knowledge on the dynamics of the concentration of ATP ([ATP]) provides important insights into the energetic state of a cell. Several genetically encoded fluorescent nanosensors for ATP were developed, which allow following the cytosolic [ATP] at high spatial and temporal resolution using fluorescence microscopy. However, to calibrate the fluorescent signal to [ATP] has remained challenging. To estimate basal cytosolic [ATP] ([ATP]0) in astrocytes, we here took advantage of two ATP nanosensors of the ATeam-family (ATeam1.03; ATeam1.03YEMK) with different affinities for ATP. Altering [ATP] by external stimuli resulted in characteristic pairs of signal changes of both nanosensors, which depend on [ATP]0. Using this dual nanosensor strategy and epifluorescence microscopy, [ATP]0 was estimated to be around 1.5 mM in primary cultures of cortical astrocytes from mice. Furthermore, in astrocytes in acutely isolated cortical slices from mice expressing both nanosensors after stereotactic injection of AAV-vectors, 2-photon microscopy revealed [ATP]0 of 0.7 mM to 1.3 mM. Finally, the change in [ATP] induced in the cytosol of cultured cortical astrocytes by application of azide, glutamate, and an increased extracellular concentration of K+ were calculated as −0.50 mM, −0.16 mM, and 0.07 mM, respectively. In summary, the dual nanosensor approach adds another option for determining the concentration of [ATP] to the increasing toolbox of fluorescent nanosensors for metabolites. This approach can also be applied to other metabolites when two sensors with different binding properties are available.
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Affiliation(s)
- Susanne Köhler
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany
| | - Hartmut Schmidt
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany
| | - Paula Fülle
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany.,Wilhelm-Ostwald-Schule, Gymnasium der Stadt Leipzig, Leipzig, Germany
| | - Johannes Hirrlinger
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany.,Department of Neurogenetics, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Ulrike Winkler
- Carl-Ludwig-Institute for Physiology, Faculty of Medicine, University Leipzig, Leipzig, Germany
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34
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Yoshinari A, Moe-Lange J, Kleist TJ, Cartwright HN, Quint DA, Ehrhardt DW, Frommer WB, Nakamura M. Using Genetically Encoded Fluorescent Biosensors for Quantitative In Vivo Imaging. Methods Mol Biol 2020; 2200:303-322. [PMID: 33175384 DOI: 10.1007/978-1-0716-0880-7_14] [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: 04/23/2023]
Abstract
Fluorescent biosensors are powerful tools for tracking analytes or cellular processes in live organisms and allowing visualization of the spatial and temporal dynamics of cellular regulators. Fluorescent protein (FP)-based biosensors are extensively employed due to their high selectivity and low invasiveness. A variety of FP-based biosensors have been engineered and applied in plant research to visualize dynamic changes in pH, redox state, concentration of molecules (ions, sugars, peptides, ATP, reactive oxygen species, and phytohormones), and activity of transporters. In this chapter, we briefly summarize reported uses of FP-based biosensors in planta and show simple methods to monitor the dynamics of intracellular Ca2+ in Arabidopsis thaliana using a ratiometric genetically encoded Ca2+ indicator, MatryoshCaMP6s.
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Affiliation(s)
- Akira Yoshinari
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Jacob Moe-Lange
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Thomas J Kleist
- Institute for Molecular Physiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Heather N Cartwright
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - David A Quint
- Center for Cellular and Biomolecular Machines (NSF-Crest), University of California, Merced, CA, USA
| | - David W Ehrhardt
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Wolf B Frommer
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Institute for Molecular Physiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.
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35
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Zemerov SD, Roose BW, Farenhem KL, Zhao Z, Stringer MA, Goldman AR, Speicher DW, Dmochowski IJ. 129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration. Anal Chem 2020; 92:12817-12824. [PMID: 32897053 PMCID: PMC7649717 DOI: 10.1021/acs.analchem.0c00967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable via a sensitive NMR technique known as hyperpolarized 129Xe chemical exchange saturation transfer (hyper-CEST). We demonstrate that RBP, with a tunable ribose-binding site and further engineered to bind xenon, enables the quantitation of ribose over a wide concentration range (nM to mM). Ribose binding induces the RBP "closed" conformation, which slows Xe exchange to a rate detectable by hyper-CEST. Such detection is remarkably specific for ribose, with the minimal background signal from endogenous sugars of similar size and structure, for example, glucose or ribose-6-phosphate. Ribose concentration was measured for mammalian cell lysate and serum, which led to estimates of low-mM ribose in a HeLa cell line. This highlights the potential for using genetically encoded periplasmic binding proteins such as RBP to measure metabolites in different biological fluids, tissues, and physiologic states.
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Affiliation(s)
- Serge D. Zemerov
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Benjamin W. Roose
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Kelsey L. Farenhem
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Madison A. Stringer
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Aaron R. Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute,
Philadelphia, PA 19104, USA
| | - David W. Speicher
- Proteomics and Metabolomics Facility, The Wistar Institute,
Philadelphia, PA 19104, USA
- Molecular and Cellular Oncogenesis Program, The Wistar
Institute, Philadelphia, PA 19104, USA
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
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36
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Martins C, Chauhan VM, Araújo M, Abouselo A, Barrias CC, Aylott JW, Sarmento B. Advanced polymeric nanotechnology to augment therapeutic delivery and disease diagnosis. Nanomedicine (Lond) 2020; 15:2287-2309. [PMID: 32945230 DOI: 10.2217/nnm-2020-0145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Therapeutic and diagnostic payloads are usually associated with properties that compromise their efficacy, such as poor aqueous solubility, short half-life, low bioavailability, nonspecific accumulation and diverse side effects. Nanotechnological solutions have emerged to circumvent some of these drawbacks, augmenting therapeutic and/or diagnostic outcomes. Nanotechnology has benefited from the rise in polymer science research for the development of novel nanosystems for therapeutic and diagnostic purposes. Polymers are a widely used class of biomaterials, with a considerable number of regulatory approvals for application in clinics. In addition to their versatility in production and functionalization, several synthetic and natural polymers demonstrate biocompatible properties that dictate their successful biological performance. This article highlights the physicochemical characteristics of a variety of natural and synthetic biocompatible polymers, as well as their role in the manufacture of nanotechnology-based systems, state-of-art applications in disease treatment and diagnosis, and current challenges in finding a way to clinics.
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Affiliation(s)
- Cláudia Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal.,School of Pharmacy, Boots Science Building, University of Nottingham, Nottingham, NG7 2RD, UK.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Ruade Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Veeren M Chauhan
- School of Pharmacy, Boots Science Building, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marco Araújo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal
| | - Amjad Abouselo
- School of Pharmacy, Boots Science Building, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Cristina C Barrias
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal
| | - Jonathan W Aylott
- School of Pharmacy, Boots Science Building, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Bruno Sarmento
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393, Porto, Portugal.,CESPU - Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra 1317, 4585-116, Gandra, Portugal
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Designing and construction of genetically encoded FRET-based nanosensor for qualitative analysis of digoxin. J Biotechnol 2020; 323:322-330. [PMID: 32937180 DOI: 10.1016/j.jbiotec.2020.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/20/2020] [Accepted: 09/12/2020] [Indexed: 11/27/2022]
Abstract
Nanobiotechnological improvements defined on the utilization of biological materials and principles have enormously partaken to revolutionize physical, chemical, and biological sciences. However, the exploration of plant nanobiotechnology is still in its outset. The search for novel tools to monitor plant biomolecules is an emerging issue for the nanobiotechnologists. Given this, a genetically encoded FRET-based nanobiosensor has been developed to monitor the popular plant cardiac glycoside - digoxin, which is used as the most common prescription drug for heart-related illnesses across the world. Digoxin is sourced from the leaves of the foxglove plant (Digitalis purpurea L.) and has a significant demand in the medical sector. Moreover, with the rising popularity of the herbal formulations in the global market, attention towards the authentication and quality control of the herbal drugs is important. Furthermore, digoxin has a very narrow therapeutic range, i.e., 0.6 nM - 2.6 nM. Therefore, strict monitoring of blood digoxin levels is necessary. Besides, previously used techniques for drug authentication and quantification of small-molecule drugs in blood samples are not the best choice available. The nanobiosensor is based on the FRET (Fluorescence Resonance Energy Transfer) mechanism, and it is constructed in such a way that it gives a changed FRET output in the presence of digoxin. Two fluorophores, enhanced cyan fluorescent protein (ECFP) and Venus, were attached on either end of the sensory domain - human nuclear receptor ROR-gamma (RORγt). The developed nanobiosensor was named as fluorescent indicator protein for digoxin, (FLIP-digoxin). The ligand binding affinity of FLIP-digoxin was calculated as 425 μM. Affinity mutants of the FLIP-digoxin were also generated to measure digoxin in wide concentration ranges. This sensor offers high-throughput qualitative analysis of digoxin in Digitalis preparations procured from local drug stores. It confirms the authenticity of the preparations through the detection of digoxin. The FLIP-1n was also able to monitor digoxin concentration in serum samples in lesser than 5 min. The nanobiosensor was found pH stable, digoxin-specific, non- interfered by the biological serum species and can perform high throughput screening of the Digitalis powder, infusion and tincture preparations.
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Koveal D, Díaz-García CM, Yellen G. Fluorescent Biosensors for Neuronal Metabolism and the Challenges of Quantitation. Curr Opin Neurobiol 2020; 63:111-121. [PMID: 32559637 PMCID: PMC7646541 DOI: 10.1016/j.conb.2020.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 01/08/2023]
Abstract
Over the past decade, genetically encoded fluorescent biosensors that report metabolic changes have become valuable tools for understanding brain metabolism. These sensors have been targeted to specific brain regions and cell types in different organisms to track multiple metabolic processes at single cell (and subcellular) resolution. Here, we review genetically encoded biosensors used to study metabolism in the brain. We particularly focus on the principles needed to use these sensors quantitatively while avoiding false inferences from variations in sensor fluorescence that arise from differences in expression level or environmental influences such as pH or temperature.
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Affiliation(s)
- Dorothy Koveal
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
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Galaz A, Cortés-Molina F, Arce-Molina R, Romero-Gómez I, Mardones GA, Felipe Barros L, San Martín A. Imaging of the Lactate/Pyruvate Ratio Using a Genetically Encoded Förster Resonance Energy Transfer Indicator. Anal Chem 2020; 92:10643-10650. [PMID: 32600029 DOI: 10.1021/acs.analchem.0c01741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ratio between the cytosolic concentrations of lactate and pyruvate is a direct readout of the balance between glycolysis and mitochondrial oxidative metabolism. Current approaches do not allow detection of the lactate/pyruvate ratio in a single readout with high spatial/temporal resolution in living systems. Using a Förster resonance energy transfer (FRET)-based screening strategy, we found that the orphan transcriptional factor LutR from Bacillus licheniformis is an endogenous sensor of the lactate/pyruvate ratio, suitable for use as a binding moiety to develop a lactate/pyruvate ratio FRET-based genetically encoded indicator, Lapronic. The sensitivity of the indicator to lactate and pyruvate was characterized through changes in the fluorescence FRET ratio and validated with isothermal titration calorimetry. Lapronic was insensitive to physiological pH and temperature and did not respond to structurally related molecules acetate and β-hydroxybutyrate or cofactors NAD+ and NADH. Lapronic was expressed in HEK 293 cells showing a homogeneous cytosolic localization and was also targeted to the mitochondrial matrix. A calibration protocol was designed to quantitatively assess the lactate/pyruvate ratio in intact mammalian cells. Purified protein from Escherichia coli showed robust stability over time and was found suitable for lactate/pyruvate ratio detection in biological samples. We envision that Lapronic will be of practical interest for basic and applied research.
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Affiliation(s)
- Alex Galaz
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | | | - Robinson Arce-Molina
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | - Ignacio Romero-Gómez
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | - Gonzalo Antonio Mardones
- Instituto de Fisiologı́a, Facultad de Medicina, Universidad Austral de Chile (UACh), Isla Teja s/n, Valdivia 5110566, Chile
| | - L Felipe Barros
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
| | - Alejandro San Martín
- Centro de Estudios Cientı́ficos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
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40
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Metabolic Regulation Analysis of Ajmalicine Biosynthesis Pathway in Catharanthus roseus (L.) G. Don Suspension Culture Using Nanosensor. Processes (Basel) 2020. [DOI: 10.3390/pr8050589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ajmalicine is one of the most popular antihypertensive drugs obtained from the root barks of Cathranthus roseus (L.) G. Don and Rauvolfia serpentine (L.) Benth. ex Kurz. It has also potential antimicrobial, cytotoxic, central depressant and antioxidant activities. As the demand for the alkaloid is significantly high, metabolic engineering approaches are being tried to increase its production in both homologous and heterologous systems. The metabolic engineering approach requires knowledge of the metabolic regulation of the alkaloid. For understanding the metabolic regulation, fluxomic analysis is important as it helps in understanding the flux of the alkaloid through the complicated metabolic pathway. The present study was conducted to analyse the flux analysis of the ajmalicine biosynthesis, using a genetically encoded Fluorescent Resonance Energy Transfer FRET-based nanosensor for ajmalicine (FLIP-Ajn). Here, we have silenced six important genes of terpenoid indole alkaloid (TIA), namely G10H, 10HGO, TDC, SLS, STR and SDG, through RNA-mediated gene silencing in different batches of C. roseus suspension cells, generating six silenced cell lines. Monitoring of the ajmalicine level was carried out using FLIP-Ajn in these silenced cell lines, with high spatial and temporal resolution. The study offers the rapid, high throughput real-time measurement of ajmalicine flux in response to the silenced TIA genes, thereby identifying the regulatory gene controlling the alkaloid flux in C. roseus suspension cells. We have reported that the STR gene encoding strictosidine synthase of the TIA pathway could be the regulatory gene of the ajmalicine biosynthesis.
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41
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Chowdhury HH. Differences in cytosolic glucose dynamics in astrocytes and adipocytes measured by FRET-based nanosensors. Biophys Chem 2020; 261:106377. [PMID: 32302866 DOI: 10.1016/j.bpc.2020.106377] [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: 02/08/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2022]
Abstract
The cellular response to fluctuations in blood glucose levels consists of integrative regulation of cell glucose uptake and glucose utilization in the cytosol, resulting in altered levels of glucose in the cytosol. Cytosolic glucose is difficult to be measured in the intact tissue, however recently methods have become available that allow measurements of glucose in single living cells with fluorescence resonance energy transfer (FRET) based protein sensors. By studying the dynamics of cytosolic glucose levels in different experimental settings, we can gain insights into the properties of plasma membrane permeability to glucose and glucose utilization in the cytosol, and how these processes are modulated by different environmental conditions, agents and enzymes. In this review, we compare the cytosolic regulation of glucose in adipocytes and astrocytes - two important regulators of energy balance and glucose homeostasis in whole body and brain, respectively, with particular emphasis on the data obtained with FRET based protein sensors as well as other biochemical and molecular approaches.
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Affiliation(s)
- Helena H Chowdhury
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, University of Ljubljana, Faculty of Medicine, 1000 Ljubljana, Slovenia; Laboratory of Cell Engineering, Celica Biomedical, 1000 Ljubljana, Slovenia.
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42
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A Non-Invasive Tool for Real-Time Measurement of Sulfate in Living Cells. Int J Mol Sci 2020; 21:ijms21072572. [PMID: 32272790 PMCID: PMC7177696 DOI: 10.3390/ijms21072572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/19/2023] Open
Abstract
Sulfur (S) is an essential element for all forms of life. It is involved in numerous essential processes because S is considered as the primary source of one of the essential amino acids, methionine, which plays an important role in biological events. For the control and regulation of sulfate in a metabolic network through fluxomics, a non-invasive tool is highly desirable that opens the door to monitor the level of the sulfate in real time and space in living cells without fractionation of the cells or tissue. Here, we engineered a FRET (fluorescence resonance energy transfer) based sensor for sulfate, which is genetically-encoded and named as FLIP-SP (Fluorescent indicator protein for sulfate). The FLIP-SP can measure the level of the sulfate in live cells. This sensor was constructed by the fusion of fluorescent proteins at the N- and C-terminus of sulfate binding protein (sbp). The FLIP-SP is highly specific to sulfate, and showed pH stability. Real-time monitoring of the level of sulfate in prokaryotic and eukaryotic cells showed sensor bio-compatibility with living cells. We expect that this sulfate sensor offers a valuable strategy in the understanding of the regulation of the flux of sulfate in the metabolic network.
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43
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Hongdusit A, Zwart PH, Sankaran B, Fox JM. Minimally disruptive optical control of protein tyrosine phosphatase 1B. Nat Commun 2020; 11:788. [PMID: 32034150 PMCID: PMC7005756 DOI: 10.1038/s41467-020-14567-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/14/2020] [Indexed: 01/13/2023] Open
Abstract
Protein tyrosine phosphatases regulate a myriad of essential subcellular signaling events, yet they remain difficult to study in their native biophysical context. Here we develop a minimally disruptive optical approach to control protein tyrosine phosphatase 1B (PTP1B)—an important regulator of receptor tyrosine kinases and a therapeutic target for the treatment of diabetes, obesity, and cancer—and we use that approach to probe the intracellular function of this enzyme. Our conservative architecture for photocontrol, which consists of a protein-based light switch fused to an allosteric regulatory element, preserves the native structure, activity, and subcellular localization of PTP1B, affords changes in activity that match those elicited by post-translational modifications inside the cell, and permits experimental analyses of the molecular basis of optical modulation. Findings indicate, most strikingly, that small changes in the activity of PTP1B can cause large shifts in the phosphorylation states of its regulatory targets. Protein tyrosine phosphatases regulate many cellular processes but are difficult to study in their native context. Here the authors develop an approach for using light to control the activity of a disease-relevant phosphatase without interfering with its native cellular organization.
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Affiliation(s)
- Akarawin Hongdusit
- Department of Chemical and Biological Engineering, University of Colorado - Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
| | - Peter H Zwart
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado - Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA.
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Yoshida T, Nakajima H, Takahashi S, Kakizuka A, Imamura H. OLIVe: A Genetically Encoded Fluorescent Biosensor for Quantitative Imaging of Branched-Chain Amino Acid Levels inside Single Living Cells. ACS Sens 2019; 4:3333-3342. [PMID: 31845569 DOI: 10.1021/acssensors.9b02067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Branched-chain amino acids (BCAAs) are essential amino acids, controlling cellular metabolic processes as signaling molecules; therefore, utilization of intracellular BCAAs may be regulated by the availability of nutrients in the environment. However, spatial and temporal regulation of intracellular BCAA concentration in response to environmental conditions has been unclear due to the lack of suitable methods for measuring BCAA concentrations inside single living cells. Here, we developed a Förster resonance energy transfer (FRET)-based genetically encoded biosensor for BCAAs, termed optical biosensor for leucine-isoleucine-valine (OLIVe). The biosensor showed approximately 2-fold changes in FRET values corresponding to BCAA concentrations. Importantly, FRET signals from HeLa cells expressing OLIVe in the cytoplasm and nucleus correlated with bulk intracellular BCAA concentrations determined from populations of cells by a biochemical method, and were decreased by knockdown of L-type amino acid transporter 1 (LAT1), a transporter for BCAAs, indicating that OLIVe can reliably report intracellular BCAA concentrations inside single living cells. We also succeeded in imaging BCAA concentrations in the mitochondria using mitochondria-targeted OLIVe. Using the BCAA imaging technique, we found apparently correlated concentrations between the cytoplasm and the mitochondria. We also found that extracellular non-BCAA amino acids affected intracellular BCAA concentrations. Of these amino acids, extracellular glutamine markedly increased intracellular BCAA concentrations in a LAT1-dependent manner. Unexpectedly, extracellular pyruvate was also found to have significant positive effects on maintaining intracellular BCAA concentrations, suggesting that the cells have pyruvate-dependent systems to import BCAAs and/or to regulate BCAA metabolism.
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Affiliation(s)
- Tomoki Yoshida
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitomi Nakajima
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Sena Takahashi
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Akira Kakizuka
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiromi Imamura
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho,
Sakyo-ku, Kyoto 606-8501, Japan
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45
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González-Gutiérrez A, Ibacache A, Esparza A, Barros LF, Sierralta J. Neuronal lactate levels depend on glia-derived lactate during high brain activity in Drosophila. Glia 2019; 68:1213-1227. [PMID: 31876077 DOI: 10.1002/glia.23772] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/13/2023]
Abstract
Lactate/pyruvate transport between glial cells and neurons is thought to play an important role in how brain cells sustain the high-energy demand that neuronal activity requires. However, the in vivo mechanisms and characteristics that underlie the transport of monocarboxylates are poorly described. Here, we use Drosophila expressing genetically encoded FRET sensors to provide an ex vivo characterization of the transport of monocarboxylates in motor neurons and glial cells from the larval ventral nerve cord. We show that lactate/pyruvate transport in glial cells is coupled to protons and is more efficient than in neurons. Glial cells maintain higher levels of intracellular lactate generating a positive gradient toward neurons. Interestingly, during high neuronal activity, raised lactate in motor neurons is dependent on transfer from glial cells mediated in part by the previously described monocarboxylate transporter Chaski, providing support for in vivo glia-to-neuron lactate shuttling during neuronal activity.
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Affiliation(s)
- Andrés González-Gutiérrez
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Andrés Ibacache
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Andrés Esparza
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Jimena Sierralta
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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46
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Singh S, Sharma MP, Alqarawi AA, Hashem A, Abd_Allah EF, Ahmad A. Real-Time Optical Detection of Isoleucine in Living Cells through a Genetically-Encoded Nanosensor. SENSORS 2019; 20:s20010146. [PMID: 31881651 PMCID: PMC6983066 DOI: 10.3390/s20010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 01/19/2023]
Abstract
Isoleucine is one of the branched chain amino acids that plays a major role in the energy metabolism of human beings and animals. However, detailed investigation of specific receptors for isoleucine has not been carried out because of the non-availability of a tool that can monitor the metabolic flux of this amino acid in live cells. This study presents a novel genetically-encoded nanosensor for real-time monitoring of isoleucine in living cells. This nanosensor was developed by sandwiching a periplasmic binding protein (LivJ) of E. coli between a fluorescent protein pair, ECFP (Enhanced Cyan Fluorescent Protein), and Venus. The sensor, named GEII (Genetically Encoded Isoleucine Indicator), was pH stable, isoleucine-specific, and had a binding affinity (Kd) of 63 ± 6 μM. The GEII successfully performed real-time monitoring of isoleucine in bacterial and yeast cells, thereby, establishing its bio-compatibility in monitoring isoleucine in living cells. As a further enhancement, in silico random mutagenesis was carried out to identify a set of viable mutations, which were subsequently experimentally verified to create a library of affinity mutants with a significantly expanded operating range (96 nM–1493 μM). In addition to its applicability in understanding the underlying functions of receptors of isoleucine in metabolic regulation, the GEII can also be used for metabolic engineering of bacteria for enhanced production of isoleucine in animal feed industries.
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Affiliation(s)
- Shruti Singh
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; (S.S.); (M.P.S.)
| | - Maheshwar Prasad Sharma
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; (S.S.); (M.P.S.)
| | - Abdulaziz A. Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.A.A.)
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia;
- Mycology and Plant Disease Survey Department, plant pathology Research Institute, ARC, Gaza 12511, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.A.A.)
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
- Correspondence:
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A high-throughput screen identifies that CDK7 activates glucose consumption in lung cancer cells. Nat Commun 2019; 10:5444. [PMID: 31784510 PMCID: PMC6884612 DOI: 10.1038/s41467-019-13334-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Elevated glucose consumption is fundamental to cancer, but selectively targeting this pathway is challenging. We develop a high-throughput assay for measuring glucose consumption and use it to screen non-small-cell lung cancer cell lines against bioactive small molecules. We identify Milciclib that blocks glucose consumption in H460 and H1975, but not in HCC827 or A549 cells, by decreasing SLC2A1 (GLUT1) mRNA and protein levels and by inhibiting glucose transport. Milciclib blocks glucose consumption by targeting cyclin-dependent kinase 7 (CDK7) similar to other CDK7 inhibitors including THZ1 and LDC4297. Enhanced PIK3CA signaling leads to CDK7 phosphorylation, which promotes RNA Polymerase II phosphorylation and transcription. Milciclib, THZ1, and LDC4297 lead to a reduction in RNA Polymerase II phosphorylation on the SLC2A1 promoter. These data indicate that our high-throughput assay can identify compounds that regulate glucose consumption and that CDK7 is a key regulator of glucose consumption in cells with an activated PI3K pathway. Many cancer cells have increased glucose consumption compared to normal cells, a feature that can be exploited therapeutically. Here, the authors carry out a chemical screen and identify compounds that selectively blocks glucose metabolism in non-small-cell lung cancer cell lines.
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Ambrin G, Ahmad M, Alqarawi AA, Hashem A, Abd Allah EF, Ahmad A. Conversion of Cytochrome P450 2D6 of Human Into a FRET-Based Tool for Real-Time Monitoring of Ajmalicine in Living Cells. Front Bioeng Biotechnol 2019; 7:375. [PMID: 31828069 PMCID: PMC6890717 DOI: 10.3389/fbioe.2019.00375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
Ajmalicine is naturally present in the root bark of Catharanthus roseus L. and Rauvolfia serpentina (L.) Benth ex.Kurz. It has been extensively utilized in the treatment of hypertension across the world. The increased demand, overconsumption, and low content of the alkaloid in the plants have raised the issue of the depletion of natural sources. The metabolic engineering approach has not been successful in improving the content of the ajmalicine because the metabolic regulation of this metabolite is not known. The regulation of a metabolite in the metabolic pathway requires a tool that can carry out real-time measurement of the flux of the metabolite in living system. Given this, the present study was conducted to develop a genetically encoded FRET-based nanosensor by engineering human Cytochrome P450-2D6, an ajmalicine binding protein. The Cytochrome P450-2D6 was sandwiched between two FRET fluorophores. The design of the nanosensor brings two fluorescent proteins in conjunction with the ajmalicine binding protein, such that it undergoes FRET (Fluorescence Resonance Energy Transfer) upon binding of the ligand. The nanosensor, named as FLIP-Ajn (Fluorescence Indicator Protein for Ajmalicine), was pH stable and ajmalicine specific. The affinity of the FLIP-Ajn was 582 μM. The FLIP-Ajn successfully performed real-time measurement of ajmalicine in prokaryotic (bacteria) and eukaryotic systems (yeast, animal cell line, and plant suspension culture), thereby, establishing its biocompatibility in monitoring of ajmalicine in living cells. Besides, several affinity mutants of the nanosensor were generated through mutations in the ajmalicine binding protein to increase the detection range of the nanosensor at varying physiological scales. The non-invasiveness and high spatial and temporal resolution of the tool holds a great significance in the bio-imaging of a highly compartmentalized metabolic pathway. The flux study of ajmalicine will help in identifying the regulatory steps involved in the synthesis of the alkaloids and, hence, will improve the production rate of ajmalicine from its natural sources.
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Affiliation(s)
- Ghazala Ambrin
- Department of Botany, Faculty of Life Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Ahmad
- Department of Physics, Syracuse University, New York, NY, United States
| | - Abdulaziz A Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Gaza, Egypt
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Science, Aligarh Muslim University, Aligarh, India
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Kostyuk AI, Demidovich AD, Kotova DA, Belousov VV, Bilan DS. Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification. Int J Mol Sci 2019; 20:E4200. [PMID: 31461959 PMCID: PMC6747460 DOI: 10.3390/ijms20174200] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 12/28/2022] Open
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) are a reliable tool for studying the various biological processes in living systems. The circular permutation of single FPs led to the development of an extensive class of biosensors that allow the monitoring of many intracellular events. In circularly permuted FPs (cpFPs), the original N- and C-termini are fused using a peptide linker, while new termini are formed near the chromophore. Such a structure imparts greater mobility to the FP than that of the native variant, allowing greater lability of the spectral characteristics. One of the common principles of creating genetically encoded biosensors is based on the integration of a cpFP into a flexible region of a sensory domain or between two interacting domains, which are selected according to certain characteristics. Conformational rearrangements of the sensory domain associated with ligand interaction or changes in the cellular parameter are transferred to the cpFP, changing the chromophore environment. In this review, we highlight the basic principles of such sensors, the history of their creation, and a complete classification of the available biosensors.
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Affiliation(s)
- Alexander I Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | | | - Daria A Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.
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Soleja N, Manzoor O, Khan P, Mohsin M. Engineering genetically encoded FRET-based nanosensors for real time display of arsenic (As 3+) dynamics in living cells. Sci Rep 2019; 9:11240. [PMID: 31375744 PMCID: PMC6677752 DOI: 10.1038/s41598-019-47682-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Arsenic poisoning has been a major concern that causes severe toxicological damages. Therefore, intricate and inclusive understanding of arsenic flux rates is required to ascertain the cellular concentration and establish the carcinogenetic mechanism of this toxicant at real time. The lack of sufficiently sensitive sensing systems has hampered research in this area. In this study, we constructed a fluorescent resonance energy transfer (FRET)-based nanosensor, named SenALiB (Sensor for Arsenic Linked Blackfoot disease) which contains a metalloregulatory arsenic-binding protein (ArsR) as the As3+ sensing element inserted between the FRET pair enhanced cyan fluorescent protein (ECFP) and Venus. SenALiB takes advantage of the ratiometic FRET readout which measures arsenic with high specificity and selectivity. SenALiB offers rapid detection response, is stable to pH changes and provides highly accurate, real-time optical readout in cell-based assays. SenALiB-676n with a binding constant (Kd) of 0.676 × 10−6 M is the most efficient affinity mutant and can be a versatile tool for dynamic measurement of arsenic concentration in both prokaryotes and eukaryotes in vivo in a non-invasive manner.
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Affiliation(s)
- Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Ovais Manzoor
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India.
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