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Marvin JS, Kokotos AC, Kumar M, Pulido C, Tkachuk AN, Yao JS, Brown TA, Ryan TA. iATPSnFR2: A high-dynamic-range fluorescent sensor for monitoring intracellular ATP. Proc Natl Acad Sci U S A 2024; 121:e2314604121. [PMID: 38748581 PMCID: PMC11126915 DOI: 10.1073/pnas.2314604121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/10/2024] [Indexed: 05/27/2024] Open
Abstract
We developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted superfolder green fluorescent protein (GFP) inserted between the ATP-binding helices of the ε-subunit of a bacterial F0-F1 ATPase. Optimizing the linkers joining the two domains resulted in a ~fivefold to sixfold improvement in the dynamic range compared to the previous-generation sensor, with excellent discrimination against other analytes, and affinity variants varying from 4 µM to 500 µM. A chimeric version of this sensor fused to either the HaloTag protein or a suitable spectrally separated fluorescent protein provides an optional ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting the sensor to nerve terminals reveals previously uncharacterized single-synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics.
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Affiliation(s)
| | - Alexandros C. Kokotos
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Mukesh Kumar
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
| | - Camila Pulido
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | | | | | | | - Timothy A. Ryan
- HHMI, Ashburn, VA20147
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
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Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL. In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor. Cell Rep 2021; 35:109284. [PMID: 34161775 DOI: 10.1016/j.celrep.2021.109284] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 03/06/2020] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Glucose is arguably the most important molecule in metabolism, and its dysregulation underlies diabetes. We describe a family of single-wavelength genetically encoded glucose sensors with a high signal-to-noise ratio, fast kinetics, and affinities varying over four orders of magnitude (1 μM to 10 mM). The sensors allow mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed ∼3-fold faster glucose changes in astrocytes. In larval Drosophila central nervous system explants, intracellular neuronal glucose fluxes suggested a rostro-caudal transport pathway in the ventral nerve cord neuropil. In zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory and pharmacological perturbations produced large changes in the brain. These sensors will enable rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.
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Affiliation(s)
- Jacob P Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Haluk Lacin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - William C Lemon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Soomin Kim
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Richard T Lee
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA; The Cardiovascular Division, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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Wegner M, Diehl V, Bittl V, de Bruyn R, Wiechmann S, Matthess Y, Hebel M, Hayes MGB, Schaubeck S, Benner C, Heinz S, Bremm A, Dikic I, Ernst A, Kaulich M. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome. eLife 2019; 8:e42549. [PMID: 30838976 PMCID: PMC6424562 DOI: 10.7554/elife.42549] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Current technologies used to generate CRISPR/Cas gene perturbation reagents are labor intense and require multiple ligation and cloning steps. Furthermore, increasing gRNA sequence diversity negatively affects gRNA distribution, leading to libraries of heterogeneous quality. Here, we present a rapid and cloning-free mutagenesis technology that can efficiently generate covalently-closed-circular-synthesized (3Cs) CRISPR/Cas gRNA reagents and that uncouples sequence diversity from sequence distribution. We demonstrate the fidelity and performance of 3Cs reagents by tailored targeting of all human deubiquitinating enzymes (DUBs) and identify their essentiality for cell fitness. To explore high-content screening, we aimed to generate the largest up-to-date gRNA library that can be used to interrogate the coding and noncoding human genome and simultaneously to identify genes, predicted promoter flanking regions, transcription factors and CTCF binding sites that are linked to doxorubicin resistance. Our 3Cs technology enables fast and robust generation of bias-free gene perturbation libraries with yet unmatched diversities and should be considered an alternative to established technologies.
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Affiliation(s)
- Martin Wegner
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Valentina Diehl
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Verena Bittl
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Rahel de Bruyn
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Svenja Wiechmann
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Project Group Translational Medicine & Pharmacology TMPFraunhofer Institute for Molecular Biology and Applied Ecology IMEFrankfurtGermany
| | - Yves Matthess
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Marie Hebel
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Michael GB Hayes
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Simone Schaubeck
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Christopher Benner
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Sven Heinz
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Anja Bremm
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Ivan Dikic
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
- Cardio-Pulmonary InstituteFrankfurt am MainGermany
| | - Andreas Ernst
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Project Group Translational Medicine & Pharmacology TMPFraunhofer Institute for Molecular Biology and Applied Ecology IMEFrankfurtGermany
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
- Cardio-Pulmonary InstituteFrankfurt am MainGermany
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Jing C, Cornish VW. Design, synthesis, and application of the trimethoprim-based chemical tag for live-cell imaging. ACTA ACUST UNITED AC 2015; 5:131-55. [PMID: 23839994 DOI: 10.1002/9780470559277.ch130019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Over the past decade, chemical tags have been developed to complement the use of fluorescent proteins in live-cell imaging. Chemical tags retain the specificity of protein labeling achieved with fluorescent proteins through genetic encoding, but provide smaller, more robust tags and modular use of organic fluorophores with high photon output and tailored functionalities. The trimethoprim-based chemical tag (TMP-tag) was initially developed based on the high affinity interaction between E. coli dihydrofolate reductase and the antibiotic trimethoprim and was subsequently rendered covalent and fluorogenic via proximity-induced protein labeling reactions. To date, the TMP-tag is one of the few chemical tags that enable intracellular protein labeling and high-resolution live-cell imaging. Here we describe the general design, chemical synthesis, and application of TMP-tag for live-cell imaging. Alternate protocols for synthesizing and using the covalent and the fluorogenic TMP-tags are also included.
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Affiliation(s)
- Chaoran Jing
- Department of Chemistry, Columbia University, New York, New York, USA
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Wright RC, Khakhar A, Eshleman JR, Ostermeier M. Advancements in the development of HIF-1α-activated protein switches for use in enzyme prodrug therapy. PLoS One 2014; 9:e114032. [PMID: 25426963 PMCID: PMC4245239 DOI: 10.1371/journal.pone.0114032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/03/2014] [Indexed: 12/25/2022] Open
Abstract
While gene-directed enzyme prodrug therapy has shown potential as a cancer therapeutic in animal and clinical trials, concerns over the efficacy, selectivity, and safety of gene delivery vehicles have restricted its advance. In an attempt to relieve some of the demands on targeted gene delivery vehicles and achieve the full potential of enzyme prodrug therapy, cancer-targeted activity can be engineered into the enzyme itself. We previously engineered a switchable prodrug-activating enzyme that selectively kills human cancer cells accumulating the cancer marker hypoxia-inducible factor-1α (HIF-1α). This HIF-1α-activated protein switch (Haps59) is designed to increase its ability to convert the prodrug 5-fluorocytosine into the chemotherapeutic 5-fluorouracil in a HIF-1α-dependent manner. However, in cancer cell lines expressing Haps59 the 5FC sensitivity difference between the presence and absence of HIF-1α was not as large as desired. In this work, we aimed to improve the cancer specificity of this switch via a directed evolution approach utilizing random mutagenesis, linker mutagenesis, and random insertion and circular permutation. We identified improved HIF-1α-activated protein switches that confer E. coli with modest increases in HIF-1α-dependent 5FC toxicity. Additionally, the current bottleneck in the development of improved HIF-1α-activated protein switches is screening switch candidates in mammalian cells. To accommodate higher throughput and reduce experimental variability, we explored the use of Flp recombinase-mediated isogenic integration in 293 cells. These experiments raised the possibility that Haps59 can be activated by other interactors of the CH1 domain, and experiments in E. coli indicated that CITED2 can also activate Haps59. Although many CH1 binding partners are also oncogenes, CH1's promiscuous binding and subsequent off-target activation of Haps59 needs to be examined under normal physiological conditions to identify off-target activators. With aberrant activating molecules identified, further directed evolution can be performed to improve the cancer specificity of HIF-1α-activated protein switches.
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Affiliation(s)
- R. Clay Wright
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Arjun Khakhar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James R. Eshleman
- Departments of Pathology and Oncology, Sol Goldman Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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