1
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Mann MM, Berger BW. A genetically-encoded biosensor for direct detection of perfluorooctanoic acid. Sci Rep 2023; 13:15186. [PMID: 37704644 PMCID: PMC10499884 DOI: 10.1038/s41598-023-41953-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
Determination of per- and polyfluoroalkyl substances (PFAS) in drinking water at the low levels set by regulatory officials has been a major focus for sensor developing researchers. However, it is becoming more apparent that detection of these contaminants in soils, foods and consumer products is relevant and necessary at part per billion and even part per million levels. Here, a fluorescent biosensor for the rapid detection of PFOA was engineered based on human liver fatty acid binding protein (hLFABP). By conjugating circularly permuted green fluorescent protein (cp.GFP) to a split hLFABP construct, the biosensor was able to detect perfluorooctanoic acid PFOA in PBS as well as environmental water samples with LODs of 236 and 330 ppb respectively. Furthermore, E. coli cells cytosolically expressing the protein-based sensor were demonstrated to quickly detect PFOA, demonstrating feasibility of whole-cell sensing. Overall, this work demonstrates a platform technology utilizing a circularly permuted GFP and split hLFABP conjugate as a label-free optical biosensor for PFOA.
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Affiliation(s)
- Madison M Mann
- Department of Chemical Engineering, University of Virginia, 102 Engineers Way, Charlottesville, VA, 22901, USA
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, 102 Engineers Way, Charlottesville, VA, 22901, USA.
- Department of Biomedical Engineering, University of Virginia, Charlottesville, USA.
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2
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Yang C, Sun J, Wu Z, Jiang M, Li D, Wang X, Zhou C, Liu X, Ren Z, Wang J, Sun M, Sun W, Gao J. FoRSR1 Is Important for Conidiation, Fusaric Acid Production, and Pathogenicity in Fusarium oxysporum f. sp. ginseng. PHYTOPATHOLOGY 2023; 113:1244-1253. [PMID: 36706002 DOI: 10.1094/phyto-10-22-0372-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The root rot disease caused by Fusarium oxysporum f. sp. ginseng is one of the most destructive diseases of ginseng, an economically important herb. However, little is known about the pathogen's toxin biosynthesis or the molecular mechanisms regulating infection of ginseng. In this study we identified and functionally characterized the FoRSR1 gene that encodes a Ras-related (RSR) small GTPase homologous to yeast Rsr1 in F. oxysporum f. sp. ginseng. Disruption of FoRSR1 resulted in a significant reduction in mycelial dry weight in liquid cultures, although vegetative growth rate was not affected on culture plates. Notably, the Forsr1 mutant exhibited blunted and swollen hyphae with multi-nucleated compartments. It produced fewer and morphologically abnormal conidia and was defective in chlamydospore formation. In infection assays with ginseng roots, the Forsr1 mutant was significantly less virulent and caused only limited necrosis at the wounding sites. Deletion of FoRSR1 also affected pigmentation, autophagy, and production of fusaric acid. Furthermore, the expression of many candidate genes involved in secondary metabolism was significantly downregulated in the mutant, suggesting that FoRSR1 is also important for secondary metabolism. Overall, our results indicated that FoRSR1 plays important roles in conidiation, vacuolar morphology, secondary metabolism, and pathogenesis in F. oxysporum f. sp. ginseng.
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Affiliation(s)
- Cui Yang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jing Sun
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Zhaoqun Wu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Maozhu Jiang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Dayong Li
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Xinjie Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Chunxiang Zhou
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Xuecheng Liu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Zhiguo Ren
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jun Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Manli Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Wenxian Sun
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China
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3
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Hu J, Li G. Recent Progress in Fluorescent Chemosensors for Protein Kinases. Chem Asian J 2022; 17:e202200182. [PMID: 35486328 DOI: 10.1002/asia.202200182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Indexed: 11/10/2022]
Abstract
Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.
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Affiliation(s)
- Jun Hu
- Fujian Agriculture and Forestry University, College of Life Sciences, No.15 Shangxiadian Road, Cangshan District, 350002, Fuzhou, CHINA
| | - Gao Li
- Minjiang University, College of Material and Chemical Engineering, CHINA
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4
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Anttila MM, Vickerman BM, Wang Q, Lawrence DS, Allbritton NL. Photoactivatable Reporter to Perform Multiplexed and Temporally Controlled Measurements of Kinase and Protease Activity in Single Cells. Anal Chem 2021; 93:16664-16672. [PMID: 34865468 PMCID: PMC8753264 DOI: 10.1021/acs.analchem.1c04225] [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] [Indexed: 12/16/2022]
Abstract
Peptide bioreporters were developed to perform multiplexed measurements of the activation of epidermal growth factor receptor kinase (EGFR), Akt kinase (Akt/protein kinase B), and proteases/peptidases in single cells. The performance characteristics of the three reporters were assessed by measuring the reporter's proteolytic stability, kinetic constants for EGFR and Akt, and dephosphorylation rate. The reporter displaying optimal performance was composed of 6-carboxyfluorescein (6-FAM) on the peptide N-terminus, an Akt substrate sequence employing a threonine phosphorylation site for Akt, followed by a tri-D arginine linker, and finally an EGFR substrate sequence bearing a phosphatase-resistant 7-(S)-hydroxy-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (L-htc) residue as the EGFR phosphorylation site. Importantly, use of a single electrophoretic condition separated the mono- and diphosphorylated products as well as proteolytic forms permitting the quantitation of multiple enzyme activities simultaneously using a single reporter. Because the Akt and EGFR substrates were linked, a known ratio (EGFR/Akt) of the reporter was loaded into cells. A photoactivatable version of the reporter was synthesized by adding two 4,5-dimethoxy-2-nitrobenzyl (DMNB) moieties to mask the EGFR and Akt phosphorylation sites. The DMNB moieties were readily photocleaved following exposure to 360 nm light, unmasking the phosphorylation sites on the reporter. The new photoactivatable reporter permitted multiplexed measurements of kinase signaling and proteolytic degradation in single cells in a temporally controlled manner. This work will facilitate the development of a new generation of multiplexed activity-based reporters capable of light-initiated measurement of enzymatic activity in single cells.
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Affiliation(s)
- Matthew M. Anttila
- Department of Chemistry, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
- Department of Bioengineering, University of Washington, Seattle, Washington, 98125
| | - Brianna M. Vickerman
- Department of Chemistry, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Qunzhao Wang
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - David S. Lawrence
- Department of Chemistry, Chapel Hill, North Carolina 27599
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
- Department of Pharmacology, School of Medicine, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, 98125
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5
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Fu Z, Dean JW, Xiong L, Dougherty MW, Oliff KN, Chen ZME, Jobin C, Garrett TJ, Zhou L. Mitochondrial transcription factor A in RORγt + lymphocytes regulate small intestine homeostasis and metabolism. Nat Commun 2021; 12:4462. [PMID: 34294718 PMCID: PMC8298438 DOI: 10.1038/s41467-021-24755-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
RORγt+ lymphocytes, including interleukin 17 (IL-17)-producing gamma delta T (γδT17) cells, T helper 17 (Th17) cells, and group 3 innate lymphoid cells (ILC3s), are important immune regulators. Compared to Th17 cells and ILC3s, γδT17 cell metabolism and its role in tissue homeostasis remains poorly understood. Here, we report that the tissue milieu shapes splenic and intestinal γδT17 cell gene signatures. Conditional deletion of mitochondrial transcription factor A (Tfam) in RORγt+ lymphocytes significantly affects systemic γδT17 cell maintenance and reduces ILC3s without affecting Th17 cells in the gut. In vivo deletion of Tfam in RORγt+ lymphocytes, especially in γδT17 cells, results in small intestine tissue remodeling and increases small intestine length by enhancing the type 2 immune responses in mice. Moreover, these mice show dysregulation of the small intestine transcriptome and metabolism with less body weight but enhanced anti-helminth immunity. IL-22, a cytokine produced by RORγt+ lymphocytes inhibits IL-13-induced tuft cell differentiation in vitro, and suppresses the tuft cell-type 2 immune circuit and small intestine lengthening in vivo, highlighting its key role in gut tissue remodeling.
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Affiliation(s)
- Zheng Fu
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Joseph W Dean
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Lifeng Xiong
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | | | - Kristen N Oliff
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Zong-Ming E Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Christian Jobin
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32608, USA
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
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6
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Kinnunen PC, Luker KE, Luker GD, Linderman JJ. Computational methods for characterizing and learning from heterogeneous cell signaling data. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 26:98-108. [PMID: 35647414 DOI: 10.1016/j.coisb.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Heterogeneity in cell signaling pathways is increasingly appreciated as a fundamental feature of cell biology and a driver of clinically relevant disease phenotypes. Understanding the causes of heterogeneity, the cellular mechanisms used to control heterogeneity, and the downstream effects of heterogeneity in single cells are all key obstacles for manipulating cellular populations and treating disease. Recent advances in genetic engineering, including multiplexed fluorescent reporters, have provided unprecedented measurements of signaling heterogeneity, but these vast data sets are often difficult to interpret, necessitating the use of computational techniques to extract meaning from the data. Here, we review recent advances in computational methods for extracting meaning from these novel data streams. In particular, we evaluate how machine learning methods related to dimensionality reduction and classification can identify structure in complex, dynamic datasets, simplifying interpretation. We also discuss how mechanistic models can be merged with heterogeneous data to understand the underlying differences between cells in a population. These methods are still being developed, but the work reviewed here offers useful applications of specific analysis techniques that could enable the translation of single-cell signaling data to actionable biological understanding.
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Affiliation(s)
- Patrick C Kinnunen
- Department of Chemical Engineering, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI, 48109-2800, USA
| | - Kathryn E Luker
- Department of Radiology, Center for Molecular Imaging, University of Michigan, 109 Zina Pitcher Place, A526 BSRB, Ann Arbor, MI, 48109-2200, USA
| | - Gary D Luker
- Department of Radiology, Center for Molecular Imaging, University of Michigan, 109 Zina Pitcher Place, A526 BSRB, Ann Arbor, MI, 48109-2200, USA.,Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA, 48109.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA, 48109
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI, 48109-2800, USA.,Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA, 48109
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7
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Tenner B, Zhang JZ, Kwon Y, Pessino V, Feng S, Huang B, Mehta S, Zhang J. FluoSTEPs: Fluorescent biosensors for monitoring compartmentalized signaling within endogenous microdomains. SCIENCE ADVANCES 2021; 7:7/21/eabe4091. [PMID: 34020947 PMCID: PMC8139597 DOI: 10.1126/sciadv.abe4091] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/01/2021] [Indexed: 05/10/2023]
Abstract
Growing evidence suggests that many essential intracellular signaling events are compartmentalized within kinetically distinct microdomains in cells. Genetically encoded fluorescent biosensors are powerful tools to dissect compartmentalized signaling, but current approaches to probe these microdomains typically rely on biosensor fusion and overexpression of critical regulatory elements. Here, we present a novel class of biosensors named FluoSTEPs (fluorescent sensors targeted to endogenous proteins) that combine self-complementing split green fluorescent protein, CRISPR-mediated knock-in, and fluorescence resonance energy transfer biosensor technology to probe compartmentalized signaling dynamics in situ. We designed FluoSTEPs for simultaneously highlighting endogenous microdomains and reporting domain-specific, real-time signaling events including kinase activities, guanosine triphosphatase activation, and second messenger dynamics in live cells. A FluoSTEP for 3',5'-cyclic adenosine monophosphate (cAMP) revealed distinct cAMP dynamics within clathrin microdomains in response to stimulation of G protein-coupled receptors, showcasing the utility of FluoSTEPs in probing spatiotemporal regulation within endogenous signaling architectures.
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Affiliation(s)
- Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jason Z Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yonghoon Kwon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Veronica Pessino
- Graduate Program of Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Siyu Feng
- The UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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8
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Exploration of 7-azaindole-coumaranone hybrids and their analogues as protein kinase inhibitors. Chem Biol Interact 2021; 343:109478. [PMID: 33905741 DOI: 10.1016/j.cbi.2021.109478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/24/2021] [Accepted: 04/12/2021] [Indexed: 01/01/2023]
Abstract
7-Azaindole has been labelled a privileged scaffold for the design of new potent inhibitors of protein kinases. In this paper, we determined the inhibition profiles of novel mono- and disubstituted derivatives of 7-azaindole-coumaranone hybrids on various disease-related protein kinases. Eight hit compounds were identified, including a potent Haspin inhibitor with an IC50 value of 0.15 μM. An interesting observation was that all active monosubstituted compounds displayed dual inhibition for Haspin and GSK-3β, while disubstituted derivatives inhibited GSK-3β and LmCK1 from Leishmania major parasite. Analyses of structure activity relationships (SARs) also revealed that mono-substitution with para-fluorobenzyloxy ring produced an equipotent inhibition of Haspin and GSK-3β. Haspin and GSK-3β are relevant targets for developing new anticancer agents while LmCK1 is an innovative target for leishmanicidal drugs. Novel compounds reported in this paper constitute promising starting points for the development of new anticancer and leishmanicidal drugs.
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9
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de Boer A, Krul L, Fehr M, Geurts L, Kramer N, Tabernero Urbieta M, van der Harst J, van de Water B, Venema K, Schütte K, Hepburn PA. Animal-free strategies in food safety & nutrition: What are we waiting for? Part I: Food safety. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.10.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Liput DJ, Nguyen TA, Augustin SM, Lee JO, Vogel SS. A Guide to Fluorescence Lifetime Microscopy and Förster's Resonance Energy Transfer in Neuroscience. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 94:e108. [PMID: 33232577 PMCID: PMC8274369 DOI: 10.1002/cpns.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorescence lifetime microscopy (FLIM) and Förster's resonance energy transfer (FRET) are advanced optical tools that neuroscientists can employ to interrogate the structure and function of complex biological systems in vitro and in vivo using light. In neurobiology they are primarily used to study protein-protein interactions, to study conformational changes in protein complexes, and to monitor genetically encoded FRET-based biosensors. These methods are ideally suited to optically monitor changes in neurons that are triggered optogenetically. Utilization of this technique by neuroscientists has been limited, since a broad understanding of FLIM and FRET requires familiarity with the interactions of light and matter on a quantum mechanical level, and because the ultra-fast instrumentation used to measure fluorescent lifetimes and resonance energy transfer are more at home in a physics lab than in a biology lab. In this overview, we aim to help neuroscientists overcome these obstacles and thus feel more comfortable with the FLIM-FRET method. Our goal is to aid researchers in the neuroscience community to achieve a better understanding of the fundamentals of FLIM-FRET and encourage them to fully leverage its powerful ability as a research tool. Published 2020. U.S. Government.
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Affiliation(s)
- Daniel J. Liput
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Tuan A. Nguyen
- Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Shana M. Augustin
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Jeong Oen Lee
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Steven S. Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Corresponding author:
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11
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Zhang JZ, Lu TW, Stolerman LM, Tenner B, Yang JR, Zhang JF, Falcke M, Rangamani P, Taylor SS, Mehta S, Zhang J. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Cell 2020; 182:1531-1544.e15. [PMID: 32846158 PMCID: PMC7502557 DOI: 10.1016/j.cell.2020.07.043] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022]
Abstract
The fidelity of intracellular signaling hinges on the organization of dynamic activity architectures. Spatial compartmentation was first proposed over 30 years ago to explain how diverse G protein-coupled receptors achieve specificity despite converging on a ubiquitous messenger, cyclic adenosine monophosphate (cAMP). However, the mechanisms responsible for spatially constraining this diffusible messenger remain elusive. Here, we reveal that the type I regulatory subunit of cAMP-dependent protein kinase (PKA), RIα, undergoes liquid-liquid phase separation (LLPS) as a function of cAMP signaling to form biomolecular condensates enriched in cAMP and PKA activity, critical for effective cAMP compartmentation. We further show that a PKA fusion oncoprotein associated with an atypical liver cancer potently blocks RIα LLPS and induces aberrant cAMP signaling. Loss of RIα LLPS in normal cells increases cell proliferation and induces cell transformation. Our work reveals LLPS as a principal organizer of signaling compartments and highlights the pathological consequences of dysregulating this activity architecture.
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Affiliation(s)
- Jason Z Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lucas M Stolerman
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica R Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Department of Physics, Humboldt University, 12489 Berlin, Germany
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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12
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Reissaus CA, Day KH, Mirmira RG, Dunn KW, Pavalko FM, Day RN. PIE-FLIM Measurements of Two Different FRET-Based Biosensor Activities in the Same Living Cells. Biophys J 2020; 118:1820-1829. [PMID: 32191861 DOI: 10.1016/j.bpj.2020.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
We report the use of pulsed interleaved excitation (PIE)-fluorescence lifetime imaging microscopy (FLIM) to measure the activities of two different biosensor probes simultaneously in single living cells. Many genetically encoded biosensors rely on the measurement of Förster resonance energy transfer (FRET) to detect changes in biosensor conformation that accompany the targeted cell signaling event. One of the most robust ways of quantifying FRET is to measure changes in the fluorescence lifetime of the donor fluorophore using FLIM. The study of complex signaling networks in living cells demands the ability to track more than one of these cellular events at the same time. Here, we demonstrate how PIE-FLIM can separate and quantify the signals from different FRET-based biosensors to simultaneously measure changes in the activity of two cell signaling pathways in the same living cells in tissues. The imaging system described here uses selectable laser wavelengths and synchronized detection gating that can be tailored and optimized for each FRET pair. Proof-of-principle studies showing simultaneous measurement of cytosolic calcium and protein kinase A activity are shown, but the PIE-FLIM approach is broadly applicable to other signaling pathways.
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Affiliation(s)
- Christopher A Reissaus
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kathleen H Day
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Raghavendra G Mirmira
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kenneth W Dunn
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana; Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Fredrick M Pavalko
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana; The Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, Indiana
| | - Richard N Day
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana; Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana.
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13
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Martin-Arevalillo R, Vernoux T. Shining light on plant hormones with genetically encoded biosensors. Biol Chem 2019; 400:477-486. [PMID: 30511920 DOI: 10.1515/hsz-2018-0310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/05/2018] [Indexed: 12/30/2022]
Abstract
Signalling molecules are produced, degraded, modified and transported throughout the development of higher organisms. Understanding their mode of action implies understanding these dynamics in vivo and in real time. Genetically encoded biosensors are being more and more used as tools to 'follow' signalling molecules and their responses inside an organism. This is the case for plants, where important progresses have been made in the development of such biosensors. Here, we summarize the main genetically encoded biosensors built for plant hormones, constructed using diverse components and steps of their signalling pathways.
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Affiliation(s)
- Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
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14
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Regulation of Neuronal Survival and Axon Growth by a Perinuclear cAMP Compartment. J Neurosci 2019; 39:5466-5480. [PMID: 31097623 DOI: 10.1523/jneurosci.2752-18.2019] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/11/2019] [Accepted: 04/10/2019] [Indexed: 12/21/2022] Open
Abstract
cAMP signaling is known to be critical in neuronal survival and axon growth. Increasingly the subcellular compartmentation of cAMP signaling has been appreciated, but outside of dendritic synaptic regulation, few cAMP compartments have been defined in terms of molecular composition or function in neurons. Specificity in cAMP signaling is conferred in large part by A-kinase anchoring proteins (AKAPs) that localize protein kinase A and other signaling enzymes to discrete intracellular compartments. We now reveal that cAMP signaling within a perinuclear neuronal compartment organized by the large multivalent scaffold protein mAKAPα promotes neuronal survival and axon growth. mAKAPα signalosome function is explored using new molecular tools designed to specifically alter local cAMP levels as studied by live-cell FRET imaging. In addition, enhancement of mAKAPα-associated cAMP signaling by isoform-specific displacement of bound phosphodiesterase is demonstrated to increase retinal ganglion cell survival in vivo in mice of both sexes following optic nerve crush injury. These findings define a novel neuronal compartment that confers cAMP regulation of neuroprotection and axon growth and that may be therapeutically targeted in disease.SIGNIFICANCE STATEMENT cAMP is a second messenger responsible for the regulation of diverse cellular processes including neuronal neurite extension and survival following injury. Signal transduction by cAMP is highly compartmentalized in large part because of the formation of discrete, localized multimolecular signaling complexes by A-kinase anchoring proteins. Although the concept of cAMP compartmentation is well established, the function and identity of these compartments remain poorly understood in neurons. In this study, we provide evidence for a neuronal perinuclear cAMP compartment organized by the scaffold protein mAKAPα that is necessary and sufficient for the induction of neurite outgrowth in vitro and for the survival of retinal ganglion cells in vivo following optic nerve injury.
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15
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Parker T, Wang KW, Manning D, Dart C. Soluble adenylyl cyclase links Ca 2+ entry to Ca 2+/cAMP-response element binding protein (CREB) activation in vascular smooth muscle. Sci Rep 2019; 9:7317. [PMID: 31086231 PMCID: PMC6514005 DOI: 10.1038/s41598-019-43821-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/30/2019] [Indexed: 12/21/2022] Open
Abstract
Ca2+-transcription coupling controls gene expression patterns that define vascular smooth muscle cell (VSMC) phenotype. Although not well understood this allows normally contractile VSMCs to become proliferative following vessel injury, a process essential for repair but which also contributes to vascular remodelling, atherogenesis and restenosis. Here we show that the Ca2+/HCO3--sensitive enzyme, soluble adenylyl cyclase (sAC), links Ca2+ influx in human coronary artery smooth muscle cells (hCASMCs) to 3',5'-cyclic adenosine monophosphate (cAMP) generation and phosphorylation of the transcription factor Ca2+/cAMP response element binding protein (CREB). Store-operated Ca2+ entry (SOCE) into hCASMCs expressing the FRET-based cAMP biosensor H187 induced a rise in cAMP that mirrored cytosolic [Ca2+]. SOCE also activated the cAMP effector, protein kinase A (PKA), as determined by the PKA reporter, AKAR4-NES, and induced phosphorylation of vasodilator-stimulated phosphoprotein (VASP) and CREB. Transmembrane adenylyl cyclase inhibition had no effect on the SOCE-induced rise in cAMP, while sAC inhibition abolished SOCE-generated cAMP and significantly reduced SOCE-induced VASP and CREB phosphorylation. This suggests that SOCE in hCASMCs activates sAC which in turn activates the cAMP/PKA/CREB axis. sAC, which is insensitive to G-protein modulation but responsive to Ca2+, pH and ATP, may therefore act as an overlooked regulatory node in vascular Ca2+-transcription coupling.
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Affiliation(s)
- Tony Parker
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Kai-Wen Wang
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Declan Manning
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Caroline Dart
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.
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16
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RAC1 Takes the Lead in Solid Tumors. Cells 2019; 8:cells8050382. [PMID: 31027363 PMCID: PMC6562738 DOI: 10.3390/cells8050382] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
Three GTPases, RAC, RHO, and Cdc42, play essential roles in coordinating many cellular functions during embryonic development, both in healthy cells and in disease conditions like cancers. We have presented patterns of distribution of the frequency of RAC1-alteration(s) in cancers as obtained from cBioPortal. With this background data, we have interrogated the various functions of RAC1 in tumors, including proliferation, metastasis-associated phenotypes, and drug-resistance with a special emphasis on solid tumors in adults. We have reviewed the activation and regulation of RAC1 functions on the basis of its sub-cellular localization in tumor cells. Our review focuses on the role of RAC1 in cancers and summarizes the regulatory mechanisms, inhibitory efficacy, and the anticancer potential of RAC1-PAK targeting agents.
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17
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Abstract
The ERK1 and ERK2 (ERK1/2) cascade is a central signaling pathway activated by a wide variety of extracellular agents that transmit the messages of G Protein Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Being such a central pathway, the activity of the cascade is well regulated, including by dynamic changes of the subcellular localization of components of the ERK1/2 cascade. In resting cells, ERK1/2 are localized in the cytosol due to their interactions with different anchoring proteins. After stimulation, ERK1/2 are phosphorylated by MEK1/2 on their regulatory TEY motif, which permits their detachment from the anchoring proteins. This detachment exposes ERK1/2 to additional phosphorylation on two serine residues (SPS motif) within the nuclear translocation signal (NTS) of the kinases. This additional phosphorylation allows ERK1/2 to interact with importin7, which consequently promotes their translocation to the nucleus. More studies are still required in order to better understand the mechanism and consequence of the nuclear translocation of ERK1/2. In this chapter, we describe some of the techniques used to study nuclear translocation of ERK1/2 in mammalian cells. We briefly mention methods such as digitonin permeabilization and cellular fractionation, as well as overexpression of reporter constructs. More thoroughly, we describe immunofluorescence, immunoprecipitation, and proximity ligation assay (PLA) approaches that are routinely used in our laboratory. Hopefully, the increase of knowledge based on these methods will open more opportunities for the identification of new therapeutic targets for diseases where the ERK1/2 cascade is dysregulated, such as cancer, neurodegenerative diseases, and diabetes.
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Affiliation(s)
- Denise A Berti
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rony Seger
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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18
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Winfree S, Hato T, Day RN. Intravital microscopy of biosensor activities and intrinsic metabolic states. Methods 2017; 128:95-104. [PMID: 28434902 PMCID: PMC5776661 DOI: 10.1016/j.ymeth.2017.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/05/2017] [Accepted: 04/18/2017] [Indexed: 01/08/2023] Open
Abstract
Intravital microscopy (IVM) is an imaging tool that is capable of detecting subcellular signaling or metabolic events as they occur in tissues in the living animal. Imaging in highly scattering biological tissues, however, is challenging because of the attenuation of signal in images acquired at increasing depths. Depth-dependent signal attenuation is the major impediment to IVM, limiting the depth from which significant data can be obtained. Therefore, making quantitative measurements by IVM requires methods that use internal calibration, or alternatively, a completely different way of evaluating the signals. Here, we describe how ratiometric imaging of genetically encoded biosensor probes can be used to make quantitative measurements of changes in the activity of cell signaling pathways. Then, we describe how fluorescence lifetime imaging can be used for label-free measurements of the metabolic states of cells within the living animal.
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Affiliation(s)
- Seth Winfree
- Department of Medicine, Division of Nephrology, Indiana University, Indianapolis, IN, USA
| | - Takashi Hato
- Department of Medicine, Division of Nephrology, Indiana University, Indianapolis, IN, USA
| | - Richard N Day
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA.
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19
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Targeting protein function: the expanding toolkit for conditional disruption. Biochem J 2017; 473:2573-89. [PMID: 27574023 PMCID: PMC5003692 DOI: 10.1042/bcj20160240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023]
Abstract
A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.
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20
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Torres-Quesada O, Röck R, Stefan E. Systematic Quantification of GPCR/cAMP-Controlled Protein Kinase A Interactions. Horm Metab Res 2017; 49:240-249. [PMID: 28427097 DOI: 10.1055/s-0042-110791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The diffusible second messenger cyclic AMP (cAMP) originates from multiple G protein-coupled receptor (GPCR) cascades activating the intracellular key effector protein kinase A (PKA). Spatially and temporally restricted cAMP-fluxes are directly sensed by macromolecular PKA complexes. The consequences are alterations of molecular interactions, which lead to activation of compartmentalized PKA phosphotransferase activities, regulating a vast array of cellular functions. To decode cell-type and cell-compartment specific PKA functions, the spatio-temporal dynamics of small molecule:protein interactions, protein:protein interactions (PPIs), cAMP-mobilization, and phosphotransferase activities need to be determined directly in the appropriate cellular context. A collection of cell-based reporters has been developed to either visualize or quantitatively measure kinase activities or PKA complex formation/dissociation. In this review, we list a collection of unimolecular and bimolecular PKA biosensors, followed by the specification of the modular design of a Renilla luciferase based protein-fragment complementation assay (PCA) platform for measuring PKA network interactions. We discuss the application spectrum of the PCA reporter to identify, quantify, and dissect dynamic and transient PKA complexes downstream of specific GPCR activities. We specify the implementation of a PCA PKA platform to systematically quantify the concurrent involvement of receptor-cAMP signaling, post-translational modifications, and kinase subunit mutations/perturbations in PKA activation. The systematic quantification of transient PKA network interactions will contribute to a better understanding how GPCR-recognized input signals are streamlined through the compartmentalized and cAMP-interacting PKA signalosome.
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Affiliation(s)
- O Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - R Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - E Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
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21
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Day RN, Tao W, Dunn KW. A simple approach for measuring FRET in fluorescent biosensors using two-photon microscopy. Nat Protoc 2016; 11:2066-80. [DOI: 10.1038/nprot.2016.121] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Depry C, Mehta S, Li R, Zhang J. Visualization of Compartmentalized Kinase Activity Dynamics Using Adaptable BimKARs. ACTA ACUST UNITED AC 2015; 22:1470-1479. [PMID: 26548610 DOI: 10.1016/j.chembiol.2015.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/14/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Abstract
The ability to monitor kinase activity dynamics in live cells greatly aids the study of how signaling events are spatiotemporally regulated. Here, we report on the adaptability of bimolecular kinase activity reporters (bimKARs) as molecular tools to enhance the real-time visualization of kinase activity. We demonstrate that the bimKAR design is truly versatile and can be used to monitor a variety of kinases, including JNK, ERK, and AMPK. Furthermore, bimKARs can have significantly enhanced dynamic ranges over their unimolecular counterparts, allowing the elucidation of previously undetectable kinase activity dynamics. Using these newly designed bimKARs, we investigate the regulation of AMPK by protein kinase A (PKA) in the plasma membrane, and demonstrate that PKA can both negatively and positively regulate AMPK activity in the same cell.
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Affiliation(s)
- Charlene Depry
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, BRF2 1120, La Jolla, CA 92093, USA
| | - Ruojing Li
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, BRF2 1120, La Jolla, CA 92093, USA.
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23
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Lindquist R, Niesner R. Intravital FRET: comprehending life at single-molecule level. Focus on "A practical method for monitoring FRET-based biosensors in living animals using two-photon microscopy". Am J Physiol Cell Physiol 2015; 309:C722-3. [PMID: 26468210 DOI: 10.1152/ajpcell.00286.2015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Raluca Niesner
- Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
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24
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The discovery of modular binding domains: building blocks of cell signalling. Nat Rev Mol Cell Biol 2015; 16:691-8. [PMID: 26420231 DOI: 10.1038/nrm4068] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell signalling - the ability of a cell to process information from the environment and change its behaviour in response - is a central property of life. Signalling depends on proteins that are assembled from a toolkit of modular domains, each of which confers a specific activity or function. The discovery of modular protein- and lipid-binding domains was a crucial turning point in understanding the logic and evolution of signalling mechanisms.
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25
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Tao W, Rubart M, Ryan J, Xiao X, Qiao C, Hato T, Davidson MW, Dunn KW, Day RN. A practical method for monitoring FRET-based biosensors in living animals using two-photon microscopy. Am J Physiol Cell Physiol 2015; 309:C724-35. [PMID: 26333599 DOI: 10.1152/ajpcell.00182.2015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/25/2015] [Indexed: 01/07/2023]
Abstract
The commercial availability of multiphoton microscope systems has nurtured the growth of intravital microscopy as a powerful technique for evaluating cell biology in the relevant context of living animals. In parallel, new fluorescent protein (FP) biosensors have become available that enable studies of the function of a wide range of proteins in living cells. Biosensor probes that exploit Förster resonance energy transfer (FRET) are among the most sensitive indicators of an array of cellular processes. However, differences between one-photon and two-photon excitation (2PE) microscopy are such that measuring FRET by 2PE in the intravital setting remains challenging. Here, we describe an approach that simplifies the use of FRET-based biosensors in intravital 2PE microscopy. Based on a systematic comparison of many different FPs, we identified the monomeric (m) FPs mTurquoise and mVenus as particularly well suited for intravital 2PE FRET studies, enabling the ratiometric measurements from linked FRET probes using a pair of experimental images collected simultaneously. The behavior of the FPs is validated by fluorescence lifetime and sensitized emission measurements of a set of FRET standards. The approach is demonstrated using a modified version of the AKAR protein kinase A biosensor, first in cells in culture, and then in hepatocytes in the liver of living mice. The approach is compatible with the most common 2PE microscope configurations and should be applicable to a variety of different FRET probes.
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Affiliation(s)
- Wen Tao
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Michael Rubart
- Riley Heart Research Center, Wells Center for Pediatric Research, and Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jennifer Ryan
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Xiao Xiao
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Chunping Qiao
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Takashi Hato
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Michael W Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, Florida
| | - Kenneth W Dunn
- Department of Medicine, Division of Nephrology, Indiana University Medical Center, Indianapolis, Indiana
| | - Richard N Day
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana
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26
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Zhou X, Clister TL, Lowry PR, Seldin MM, Wong GW, Zhang J. Dynamic Visualization of mTORC1 Activity in Living Cells. Cell Rep 2015; 10:1767-1777. [PMID: 25772363 DOI: 10.1016/j.celrep.2015.02.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 01/15/2015] [Accepted: 02/09/2015] [Indexed: 12/18/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) senses diverse signals to regulate cell growth and metabolism. It has become increasingly clear that mTORC1 activity is regulated in time and space inside the cell, but direct interrogation of such spatiotemporal regulation is challenging. Here, we describe a genetically encoded mTORC1 activity reporter (TORCAR) that exhibits a change in FRET in response to phosphorylation by mTORC1. Co-imaging mTORC1 activity and calcium dynamics revealed that a growth-factor-induced calcium transient contributes to mTORC1 activity. Dynamic activity maps generated with the use of subcellularly targeted TORCAR uncovered mTORC1 activity not only in cytosol and at the lysosome but also in the nucleus and at the plasma membrane. Furthermore, a wide distribution of activities was observed upon growth factor stimulation, whereas leucine ester, an amino acid surrogate, induces more compartmentalized activities at the lysosome and in the nucleus. Thus, mTORC1 activities are spatiotemporally regulated in a signal-specific manner.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Terri L Clister
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pamela R Lowry
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marcus M Seldin
- Department of Physiology and Center for Metabolism and Obesity Research, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - G William Wong
- Department of Physiology and Center for Metabolism and Obesity Research, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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27
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Kellenberger CA, Hammond MC. In vitro analysis of riboswitch-Spinach aptamer fusions as metabolite-sensing fluorescent biosensors. Methods Enzymol 2014; 550:147-72. [PMID: 25605385 DOI: 10.1016/bs.mie.2014.10.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The development of fluorescent biosensors has been motivated by the interest to monitor and measure the levels of specific metabolites in live cells in real time. Common approaches include fusing a protein-based receptor to fluorescent proteins or synthesizing a small molecule reactive probe. Natural metabolite-sensing riboswitches also have been used in reporter-based systems that take advantage of ligand-dependent regulation of downstream gene expression. More recently, it has been shown that RNA-based fluorescent biosensors can be generated by fusing a riboswitch aptamer to the in vitro selected Spinach aptamer, which binds a cell-permeable and conditionally fluorescent molecule. Here, we describe methods to design, prepare, and analyze riboswitch-Spinach aptamer fusion RNAs for ligand-dependent activation of fluorescence in vitro. Examples of procedures to measure fluorescence activation, ligand binding selectivity and affinity, and binding kinetics are given for a cyclic di-GMP-responsive biosensor. The relative ease of in vitro RNA synthesis and purification should make this method accessible to other researchers interested in developing riboswitch-based fluorescent biosensors.
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Affiliation(s)
| | - Ming C Hammond
- Department of Chemistry, University of California, Berkeley, California, USA; Department of Molecular & Cell Biology, University of California, Berkeley, California, USA.
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28
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Abstract
We have come a long way in the 55 years since Edmond Fischer and the late Edwin Krebs discovered that the activity of glycogen phosphorylase is regulated by reversible protein phosphorylation. Many of the fundamental molecular mechanisms that operate in biological signaling have since been characterized and the vast web of interconnected pathways that make up the cellular signaling network has been mapped in considerable detail. Nonetheless, it is important to consider how fast this field is still moving and the issues at the current boundaries of our understanding. One must also appreciate what experimental strategies have allowed us to attain our present level of knowledge. We summarize here some key issues (both conceptual and methodological), raise unresolved questions, discuss potential pitfalls, and highlight areas in which our understanding is still rudimentary. We hope these wide-ranging ruminations will be useful to investigators who carry studies of signal transduction forward during the rest of the 21st century.
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29
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Sands B, Jenkins P, Peria WJ, Naivar M, Houston JP, Brent R. Measuring and sorting cell populations expressing isospectral fluorescent proteins with different fluorescence lifetimes. PLoS One 2014; 9:e109940. [PMID: 25302964 PMCID: PMC4193854 DOI: 10.1371/journal.pone.0109940] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/04/2014] [Indexed: 01/03/2023] Open
Abstract
Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP's fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼1.5 ns vs ∼3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a “pseudophasor” that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation.
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Affiliation(s)
- Bryan Sands
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Patrick Jenkins
- Department of Chemical Engineering, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - William J. Peria
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mark Naivar
- Darkling X, LLC, Los Alamos, New Mexico, United States of America
| | - Jessica P. Houston
- Department of Chemical Engineering, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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30
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Davis DM, Purvis JE. Computational analysis of signaling patterns in single cells. Semin Cell Dev Biol 2014; 37:35-43. [PMID: 25263011 DOI: 10.1016/j.semcdb.2014.09.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/11/2014] [Accepted: 09/13/2014] [Indexed: 01/19/2023]
Abstract
Signaling proteins are flexible in both form and function. They can bind to multiple molecular partners and integrate diverse types of cellular information. When imaged by time-lapse microscopy, many signaling proteins show complex patterns of activity or localization that vary from cell to cell. This heterogeneity is so prevalent that it has spurred the development of new computational strategies to analyze single-cell signaling patterns. A collective observation from these analyses is that cells appear less heterogeneous when their responses are normalized to, or synchronized with, other single-cell measurements. In many cases, these transformed signaling patterns show distinct dynamical trends that correspond with predictable phenotypic outcomes. When signaling mechanisms are unclear, computational models can suggest putative molecular interactions that are experimentally testable. Thus, computational analysis of single-cell signaling has not only provided new ways to quantify the responses of individual cells, but has helped resolve longstanding questions surrounding many well-studied human signaling proteins including NF-κB, p53, ERK1/2, and CDK2. A number of specific challenges lie ahead for single-cell analysis such as quantifying the contribution of non-cell autonomous signaling as well as the characterization of protein signaling dynamics in vivo.
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Affiliation(s)
- Denise M Davis
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, United States
| | - Jeremy E Purvis
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, United States.
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31
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Deng Y, Alicea-Velázquez NL, Bannwarth L, Lehtonen SI, Boggon TJ, Cheng HC, Hytönen VP, Turk BE. Global analysis of human nonreceptor tyrosine kinase specificity using high-density peptide microarrays. J Proteome Res 2014; 13:4339-46. [PMID: 25164267 PMCID: PMC4184454 DOI: 10.1021/pr500503q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Protein
kinases phosphorylate substrates in the context of specific
phosphorylation site sequence motifs. The knowledge of the specific
sequences that are recognized by kinases is useful for mapping sites
of phosphorylation in protein substrates and facilitates the generation
of model substrates to monitor kinase activity. Here, we have adapted
a positional scanning peptide library method to a microarray format
that is suitable for the rapid determination of phosphorylation site
motifs for tyrosine kinases. Peptide mixtures were immobilized on
glass slides through a layer of a tyrosine-free Y33F mutant avidin
to facilitate the analysis of phosphorylation by radiolabel assay.
A microarray analysis provided qualitatively similar results in comparison
with the solution phase peptide library “macroarray”
method. However, much smaller quantities of kinases were required
to phosphorylate peptides on the microarrays, which thus enabled a
proteome scale analysis of kinase specificity. We illustrated this
capability by microarray profiling more than 80% of the human nonreceptor
tyrosine kinases (NRTKs). Microarray results were used to generate
a universal NRTK substrate set of 11 consensus peptides for in vitro
kinase assays. Several substrates were highly specific for their cognate
kinases, which should facilitate their incorporation into kinase-selective
biosensors.
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Affiliation(s)
- Yang Deng
- Department of Pharmacology, Yale University School of Medicine , New Haven, Connecticut 06520, United States
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32
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Irannejad R, Kotowski SJ, von Zastrow M. Investigating signaling consequences of GPCR trafficking in the endocytic pathway. Methods Enzymol 2014; 535:403-18. [PMID: 24377936 DOI: 10.1016/b978-0-12-397925-4.00023-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ligand-dependent regulation of adenylyl cyclase by the large family of seven-transmembrane G protein-coupled receptors (GPCRs) represents a deeply conserved and widely deployed cellular signaling mechanism. Studies of adenylyl cyclase regulation by catecholamine receptors have led to a remarkably detailed understanding of the basic biochemistry of G protein-linked signal transduction and have elaborated numerous mechanisms of regulation. Endocytosis of GPCRs plays a significant role in controlling longer-term cellular responses, such as under conditions of prolonged or repeated receptor activation occurring over a course of hours or more. It has been more challenging to investigate regulatory effects occurring over shorter time intervals, within the minutes to tens of minutes spanning the time course of many acute cyclic AMP (cAMP)-mediated signaling processes. A main reason for this is that biochemical methods used traditionally to assay changes in cytoplasmic cAMP concentration are limited in spatiotemporal resolution and typically require perturbing cellular structure and/or function for implementation. Recent developments in engineering genetically encoded cAMP biosensors linked to optical readouts, which can be expressed in cells or tissues and detected without cellular disruption or major functional perturbation, represent a significant step toward overcoming these limitations. Here, we describe the application of two such cAMP biosensors, one based on enzyme complementation and luminescence detection and another using Förster resonance energy transfer and fluorescence detection. We focus on applying these approaches to investigate cAMP signaling by catecholamine receptors and then on combining these analytical approaches with manipulations of receptor endocytic trafficking.
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Affiliation(s)
- Roshanak Irannejad
- Department of Psychiatry, University of California School of Medicine, San Francisco, California, USA; Department of Cellular & Molecular Pharmacology, University of California School of Medicine, San Francisco, California, USA
| | - Sarah J Kotowski
- Department of Psychiatry, University of California School of Medicine, San Francisco, California, USA; Department of Cellular & Molecular Pharmacology, University of California School of Medicine, San Francisco, California, USA
| | - Mark von Zastrow
- Department of Psychiatry, University of California School of Medicine, San Francisco, California, USA; Department of Cellular & Molecular Pharmacology, University of California School of Medicine, San Francisco, California, USA.
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33
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Vetter ML, Zhang Z, Liu S, Wang J, Cho H, Zhang J, Zhang W, Gray NS, Yang PL. Fluorescent visualization of Src by using dasatinib-BODIPY. Chembiochem 2014; 15:1317-24. [PMID: 24828915 DOI: 10.1002/cbic.201402010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 12/12/2022]
Abstract
Many biological experiments are not compatible with the use of immunofluorescence, genetically encoded fluorescent tags, or FRET-based reporters. Conjugation of existing kinase inhibitors to cell-permeable fluorophores can provide a generalized approach to develop fluorescent probes of intracellular kinases. Here, we report the development of a small molecule probe of Src through conjugation of BODIPY to two well-established dual Src-Abl kinase inhibitors, dasatinib and saracatinib. We show that this approach is not successful for saracatinib but that dasatinib-BODIPY largely retains the biological activity of its parent compound and can be used to monitor the presence of Src kinase in individual cells by flow cytometry. It can also be used to track the localization of Src by fixed and live-cell fluorescence microscopy. This strategy could enable generation of additional kinase-specific probes useful in systems not amenable to genetic manipulation or could be used together with fluorescent proteins to enable a multiplexed assay readout.
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Affiliation(s)
- Michael L Vetter
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 (USA)
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34
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Huang PC, Hsiao YT, Kao SY, Chen CF, Chen YC, Chiang CW, Lee CF, Lu JC, Chern Y, Wang CT. Adenosine A(2A) receptor up-regulates retinal wave frequency via starburst amacrine cells in the developing rat retina. PLoS One 2014; 9:e95090. [PMID: 24777042 PMCID: PMC4002430 DOI: 10.1371/journal.pone.0095090] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/23/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Developing retinas display retinal waves, the patterned spontaneous activity essential for circuit refinement. During the first postnatal week in rodents, retinal waves are mediated by synaptic transmission between starburst amacrine cells (SACs) and retinal ganglion cells (RGCs). The neuromodulator adenosine is essential for the generation of retinal waves. However, the cellular basis underlying adenosine's regulation of retinal waves remains elusive. Here, we investigated whether and how the adenosine A(2A) receptor (A(2A)R) regulates retinal waves and whether A(2A)R regulation of retinal waves acts via presynaptic SACs. METHODOLOGY/PRINCIPAL FINDINGS We showed that A(2A)R was expressed in the inner plexiform layer and ganglion cell layer of the developing rat retina. Knockdown of A(2A)R decreased the frequency of spontaneous Ca²⁺ transients, suggesting that endogenous A(2A)R may up-regulate wave frequency. To investigate whether A(2A)R acts via presynaptic SACs, we targeted gene expression to SACs by the metabotropic glutamate receptor type II promoter. Ca²⁺ transient frequency was increased by expressing wild-type A(2A)R (A2AR-WT) in SACs, suggesting that A(2A)R may up-regulate retinal waves via presynaptic SACs. Subsequent patch-clamp recordings on RGCs revealed that presynaptic A(2A)R-WT increased the frequency of wave-associated postsynaptic currents (PSCs) or depolarizations compared to the control, without changing the RGC's excitability, membrane potentials, or PSC charge. These findings suggest that presynaptic A(2A)R may not affect the membrane properties of postsynaptic RGCs. In contrast, by expressing the C-terminal truncated A(2A)R mutant (A(2A)R-ΔC) in SACs, the wave frequency was reduced compared to the A(2A)R-WT, but was similar to the control, suggesting that the full-length A(2A)R in SACs is required for A(2A)R up-regulation of retinal waves. CONCLUSIONS/SIGNIFICANCE A(2A)R up-regulates the frequency of retinal waves via presynaptic SACs, requiring its full-length protein structure. Thus, by coupling with the downstream intracellular signaling, A(2A)R may have a great capacity to modulate patterned spontaneous activity during neural circuit refinement.
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Affiliation(s)
- Pin-Chien Huang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Tien Hsiao
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Shao-Yen Kao
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ching-Feng Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Chieh Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chung-Wei Chiang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chien-fei Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Juu-Chin Lu
- Department of Physiology and Pharmacology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Yijuang Chern
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chih-Tien Wang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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35
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Aye-Han NN, Zhang J. A multiparameter live cell imaging approach to monitor cyclic AMP and protein kinase A dynamics in parallel. Methods Mol Biol 2014; 1071:207-15. [PMID: 24052391 DOI: 10.1007/978-1-62703-622-1_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Parallel detection of signaling activities allows us to correlate activity dynamics between signaling molecules. In this review, we detail a multiparameter live cell imaging method to monitor 3',5'-cyclic adenosine monophosphate (cAMP) levels and protein kinase A (PKA) activities in parallel.
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Affiliation(s)
- Nwe-Nwe Aye-Han
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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36
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Wrapped around the heart. Nature 2014; 507:43-4. [DOI: 10.1038/507043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Hamers D, van Voorst Vader L, Borst JW, Goedhart J. Development of FRET biosensors for mammalian and plant systems. PROTOPLASMA 2014; 251:333-347. [PMID: 24337770 DOI: 10.1007/s00709-013-0590-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
Genetically encoded biosensors are increasingly used in visualising signalling processes in different organisms. Sensors based on green fluorescent protein technology are providing a great opportunity for using Förster resonance energy transfer (FRET) as a tool that allows for monitoring dynamic processes in living cells. The development of these FRET biosensors requires careful selection of fluorophores, substrates and recognition domains. In this review, we will discuss recent developments, strategies to create and optimise FRET biosensors and applications of FRET-based biosensors for use in the two major eukaryotic kingdoms and elaborate on different methods for FRET detection.
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Affiliation(s)
- Danny Hamers
- Laboratory of Biochemistry and Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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38
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Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation. Sci Rep 2014; 4:4219. [PMID: 24573109 PMCID: PMC3936235 DOI: 10.1038/srep04219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 02/03/2014] [Indexed: 11/08/2022] Open
Abstract
Here we describe a fluctuation-based method to quantify how protein oligomerisation modulates signalling activity of a multifunctional protein. By recording fluorescence lifetime imaging microscopy (FLIM) data of a FRET biosensor in a format that enables concomitant phasor and cross Number and Brightness (cN&B) analysis, we measure the nuclear dynamics of a Rac1 FRET biosensor and assess how Rac1 homo-oligomers (N&B) regulate Rac1 activity (hetero-oligomerisation with the biosensor affinity reagent, PBD, by FLIM-FRET) or interaction with an unknown binding partner (cN&B). The high spatiotemporal resolution of this method allowed us to discover that upon DNA damage monomeric and active Rac1 in the nucleus is segregated from dimeric and inactive Rac1 in the cytoplasm. This reorganisation requires Rac1 GTPase activity and is associated with an importin-α2 redistribution. Only with this multiplexed approach can we assess the oligomeric state a molecular complex must form in order to regulate a complex signalling network.
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39
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Newman RH, Zhang J. The design and application of genetically encodable biosensors based on fluorescent proteins. Methods Mol Biol 2014; 1071:1-16. [PMID: 24052376 DOI: 10.1007/978-1-62703-622-1_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
To track the activity of cellular signaling molecules within the endogenous cellular environment, researchers have developed a diverse set of genetically encodable fluorescent biosensors. These sensors, which can be targeted to specific subcellular regions to monitor specific pools of a given signaling molecule in real time, rely upon conformational changes in a sensor domain to alter the photophysical properties of green fluorescent protein (GFP) family members. In this introductory chapter, we first discuss the properties of GFP family members before turning our attention to the design and application of genetically encodable fluorescent biosensors to live cell imaging.
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Affiliation(s)
- Robert H Newman
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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40
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Leavesley SJ, Britain AL, Cichon LK, Nikolaev VO, Rich TC. Assessing FRET using spectral techniques. Cytometry A 2013; 83:898-912. [PMID: 23929684 DOI: 10.1002/cyto.a.22340] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/13/2013] [Accepted: 06/28/2013] [Indexed: 01/21/2023]
Abstract
Förster resonance energy transfer (FRET) techniques have proven invaluable for probing the complex nature of protein-protein interactions, protein folding, and intracellular signaling events. These techniques have traditionally been implemented with the use of one or more fluorescence band-pass filters, either as fluorescence microscopy filter cubes, or as dichroic mirrors and band-pass filters in flow cytometry. In addition, new approaches for measuring FRET, such as fluorescence lifetime and acceptor photobleaching, have been developed. Hyperspectral techniques for imaging and flow cytometry have also shown to be promising for performing FRET measurements. In this study, we have compared traditional (filter-based) FRET approaches to three spectral-based approaches: the ratio of acceptor-to-donor peak emission, linear spectral unmixing, and linear spectral unmixing with a correction for direct acceptor excitation. All methods are estimates of FRET efficiency, except for one-filter set and three-filter set FRET indices, which are included for consistency with prior literature. In the first part of this study, spectrofluorimetric data were collected from a CFP-Epac-YFP FRET probe that has been used for intracellular cAMP measurements. All comparisons were performed using the same spectrofluorimetric datasets as input data, to provide a relevant comparison. Linear spectral unmixing resulted in measurements with the lowest coefficient of variation (0.10) as well as accurate fits using the Hill equation. FRET efficiency methods produced coefficients of variation of less than 0.20, while FRET indices produced coefficients of variation greater than 8.00. These results demonstrate that spectral FRET measurements provide improved response over standard, filter-based measurements. Using spectral approaches, single-cell measurements were conducted through hyperspectral confocal microscopy, linear unmixing, and cell segmentation with quantitative image analysis. Results from these studies confirmed that spectral imaging is effective for measuring subcellular, time-dependent FRET dynamics and that additional fluorescent signals can be readily separated from FRET signals, enabling multilabel studies of molecular interactions. © 2013 International Society for Advancement of Cytometry.
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Affiliation(s)
- Silas J Leavesley
- Department of Chemical and Biomolecular Engineering, University of South Alabama, Mobile, Alabama, 36688; Department of Pharmacology, University of South Alabama, Mobile, Alabama, 36688
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Erard M, Fredj A, Pasquier H, Beltolngar DB, Bousmah Y, Derrien V, Vincent P, Merola F. Minimum set of mutations needed to optimize cyan fluorescent proteins for live cell imaging. ACTA ACUST UNITED AC 2013. [DOI: 10.1039/c2mb25303h] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Höckendorf B, Thumberger T, Wittbrodt J. Quantitative Analysis of Embryogenesis: A Perspective for Light Sheet Microscopy. Dev Cell 2012; 23:1111-20. [DOI: 10.1016/j.devcel.2012.10.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/04/2012] [Accepted: 10/04/2012] [Indexed: 01/06/2023]
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43
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Hum JM, Siegel AP, Pavalko FM, Day RN. Monitoring biosensor activity in living cells with fluorescence lifetime imaging microscopy. Int J Mol Sci 2012; 13:14385-400. [PMID: 23203070 PMCID: PMC3509586 DOI: 10.3390/ijms131114385] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 10/27/2012] [Accepted: 11/01/2012] [Indexed: 11/21/2022] Open
Abstract
Live-cell microscopy is now routinely used to monitor the activities of the genetically encoded biosensor proteins that are designed to directly measure specific cell signaling events inside cells, tissues, or organisms. Most fluorescent biosensor proteins rely on Förster resonance energy transfer (FRET) to report conformational changes in the protein that occur in response to signaling events, and this is commonly measured with intensity-based ratiometric imaging methods. An alternative method for monitoring the activities of the FRET-based biosensor proteins is fluorescence lifetime imaging microscopy (FLIM). FLIM measurements are made in the time domain, and are not affected by factors that commonly limit intensity measurements. In this review, we describe the use of the digital frequency domain (FD) FLIM method for the analysis of FRET signals. We illustrate the methods necessary for the calibration of the FD FLIM system, and demonstrate the analysis of data obtained from cells expressing "FRET standard" fusion proteins. We then use the FLIM-FRET approach to monitor the changes in activities of two different biosensor proteins in specific regions of single living cells. Importantly, the factors required for the accurate determination and reproducibility of lifetime measurements are described in detail.
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Affiliation(s)
- Julia M. Hum
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Dr., MS 333, Indianapolis, IN 46202, USA; E-Mails: (J.M.H.); (A.P.S.); (F.M.P.)
| | - Amanda P. Siegel
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Dr., MS 333, Indianapolis, IN 46202, USA; E-Mails: (J.M.H.); (A.P.S.); (F.M.P.)
| | - Fredrick M. Pavalko
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Dr., MS 333, Indianapolis, IN 46202, USA; E-Mails: (J.M.H.); (A.P.S.); (F.M.P.)
| | - Richard N. Day
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Dr., MS 333, Indianapolis, IN 46202, USA; E-Mails: (J.M.H.); (A.P.S.); (F.M.P.)
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