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Frei MS, Mehta S, Zhang J. Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism. Annu Rev Biophys 2024; 53:275-297. [PMID: 38346245 DOI: 10.1146/annurev-biophys-030722-021359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of cell signaling and metabolism, as they allow for live-cell measurements with high spatiotemporal resolution. This success has spurred the development of tailor-made biosensors that enable the study of dynamic phenomena on different timescales and length scales. In this review, we discuss different approaches to enhancing and developing new biosensors. We summarize the technologies used to gain structural insights into biosensor design and comment on useful screening technologies. Furthermore, we give an overview of different applications where biosensors have led to key advances over recent years. Finally, we give our perspective on where future work is bound to make a large impact.
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Affiliation(s)
- Michelle S Frei
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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2
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Chai F, Fujii H, Le GNT, Lin C, Ota K, Lin KM, Pham LMT, Zou P, Drobizhev M, Nasu Y, Terai T, Bito H, Campbell RE. Development of an miRFP680-Based Fluorescent Calcium Ion Biosensor Using End-Optimized Transposons. ACS Sens 2024; 9:3394-3402. [PMID: 38822813 PMCID: PMC11218748 DOI: 10.1021/acssensors.4c00727] [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: 03/29/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
The development of new or improved single fluorescent protein (FP)-based biosensors (SFPBs), particularly those with excitation and emission at near-infrared wavelengths, is important for the continued advancement of biological imaging applications. In an effort to accelerate the development of new SFPBs, we report modified transposons for the transposase-based creation of libraries of FPs randomly inserted into analyte binding domains, or vice versa. These modified transposons feature ends that are optimized to minimize the length of the linkers that connect the FP to the analyte binding domain. We rationalized that shorter linkers between the domains should result in more effective allosteric coupling between the analyte binding-dependent conformational change in the binding domain and the fluorescence modulation of the chromophore of the FP domain. As a proof of concept, we employed end-modified Mu transposons for the discovery of SFPB prototypes based on the insertion of two circularly permuted red FPs (mApple and FusionRed) into binding proteins for l-lactate and spermidine. Using an analogous approach, we discovered calcium ion (Ca2+)-specific SFPBs by random insertion of calmodulin (CaM)-RS20 into miRFP680, a particularly bright near-infrared (NIR) FP based on a biliverdin (BV)-binding fluorescent protein. Starting from an miRFP680-based Ca2+ biosensor prototype, we performed extensive directed evolution, including under BV-deficient conditions, to create highly optimized biosensors designated the NIR-GECO3 series. We have extensively characterized the NIR-GECO3 series and explored their utility for biological Ca2+ imaging. The methods described in this work will serve to accelerate SFPB development and open avenues for further exploration and optimization of SFPBs across a spectrum of biological applications.
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Affiliation(s)
- Fu Chai
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hajime Fujii
- Department
of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Giang N. T. Le
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Chang Lin
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Keisuke Ota
- Department
of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Karl Matthew Lin
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Lam M. T. Pham
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Peng Zou
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mikhail Drobizhev
- Department
of Microbiology and Cell Biology, Montana
State University, Bozeman, Montana 59717, United States
| | - Yusuke Nasu
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO,
Japan Science and Technology Agency,
Chiyoda-ku, Tokyo 102-0075, Japan
| | - Takuya Terai
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Haruhiko Bito
- Department
of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Robert E. Campbell
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- CERVO
Brain Research Center and Department of Biochemistry, Microbiology,
and Bioinformatics, Université Laval, Québec, Québec G1 V 0A6, Canada
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3
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Frei MS, Sanchez SA, Liu L, Schneider F, Wang Z, Hakozaki H, Li Y, Lyons AC, Rohm TV, Olefsky JM, Shi L, Schöneberg J, Fraser SE, Mehta S, Wang Y, Zhang J. Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579766. [PMID: 38370804 PMCID: PMC10871310 DOI: 10.1101/2024.02.10.579766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Fluorescent biosensors revolutionized biomedical science by enabling the direct measurement of signaling activities in living cells, yet the current technology is limited in resolution and dimensionality. Here, we introduce highly sensitive chemigenetic kinase activity biosensors that combine the genetically encodable self-labeling protein tag HaloTag7 with bright far-red-emitting synthetic fluorophores. This technology enables five-color biosensor multiplexing, 4D activity imaging, and functional super-resolution imaging via stimulated emission depletion (STED) microscopy.
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Affiliation(s)
- Michelle S. Frei
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Samantha A. Sanchez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Longwei Liu
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Falk Schneider
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zichen Wang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yajuan Li
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Theresa V. Rohm
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jerrold M. Olefsky
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lingyan Shi
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Johannes Schöneberg
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Scott E. Fraser
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Yingxiao Wang
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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4
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Roelle S, Kamath ND, Matreyek KA. Mammalian Genomic Manipulation with Orthogonal Bxb1 DNA Recombinase Sites for the Functional Characterization of Protein Variants. ACS Synth Biol 2023; 12:3352-3365. [PMID: 37922210 PMCID: PMC10661055 DOI: 10.1021/acssynbio.3c00355] [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: 06/10/2023] [Revised: 09/22/2023] [Accepted: 10/19/2023] [Indexed: 11/05/2023]
Abstract
The Bxb1 bacteriophage serine DNA recombinase is an efficient tool for engineering recombinant DNA into the genomes of cultured cells. Generally, a single engineered "landing pad" site is introduced into the cell genome, permitting the integration of transgenic circuits or libraries of transgene variants. While sufficient for many studies, the extent of genetic manipulation possible with a single recombinase site is limiting and insufficient for more complex cell-based assays. Here, we harnessed two orthogonal Bxb1 recombinase sites to enable alternative avenues for using mammalian synthetic biology to characterize transgenic protein variants. By designing plasmids flanked by a second pair of auxiliary recombination sites, we demonstrate that we can avoid the genomic integration of undesirable bacterial DNA elements using the same starting cells engineered for whole-plasmid integration. We also created "double landing pad" cells simultaneously harboring two orthogonal Bxb1 recombinase sites at separate genomic loci, allowing complex cell-based genetic assays. Integration of a genetically encoded calcium indicator allowed for the real-time monitoring of intracellular calcium signaling dynamics, including kinetic perturbations that occur upon overexpression of the wild-type or variant version of the calcium signaling relay protein STIM1. A panel of missense mutants of the HIV-1 accessory protein Vif was paired with various paralogs within the human Apobec3 innate immune protein family to identify combinations capable or incapable of interacting within cells. These cells allow transgenic protein variant libraries to be readily paired with assay-specific protein partners or biosensors, enabling new functional readouts for large-scale genetic assays for protein function.
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Affiliation(s)
- Sarah
M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Nisha D. Kamath
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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5
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In vivo protein-based biosensors: seeing metabolism in real time. Trends Biotechnol 2023; 41:19-26. [PMID: 35918219 DOI: 10.1016/j.tibtech.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 12/31/2022]
Abstract
Biological homeostasis is a dynamic and elastic equilibrium of countless interlinked biochemical reactions. A key goal of life sciences is to understand these dynamics; bioengineers seek to reconfigure such networks. Both goals require the ability to monitor the concentration of individual intracellular metabolites with sufficient spatiotemporal resolution. To achieve this, a range of protein or protein/DNA signalling circuits with optical readouts have been constructed. Protein biosensors can provide quantitative information at subsecond temporal and suborganelle spatial resolution. However, their construction is fraught with difficulties related to integrating the affinity- and selectivity-endowing components with the signal reporters. We argue that development of efficient approaches for construction of chemically induced dimerisation systems and reporter domains with large dynamic ranges will solve these problems.
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6
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Monitoring glycolytic dynamics in single cells using a fluorescent biosensor for fructose 1,6-bisphosphate. Proc Natl Acad Sci U S A 2022; 119:e2204407119. [PMID: 35881794 PMCID: PMC9351453 DOI: 10.1073/pnas.2204407119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular metabolism is regulated over space and time to ensure that energy production is efficiently matched with consumption. Fluorescent biosensors are useful tools for studying metabolism as they enable real-time detection of metabolite abundance with single-cell resolution. For monitoring glycolysis, the intermediate fructose 1,6-bisphosphate (FBP) is a particularly informative signal as its concentration is strongly correlated with flux through the whole pathway. Using GFP insertion into the ligand-binding domain of the Bacillus subtilis transcriptional regulator CggR, we developed a fluorescent biosensor for FBP termed HYlight. We demonstrate that HYlight can reliably report the real-time dynamics of glycolysis in living cells and tissues, driven by various metabolic or pharmacological perturbations, alone or in combination with other physiologically relevant signals. Using this sensor, we uncovered previously unknown aspects of β-cell glycolytic heterogeneity and dynamics.
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7
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Jackson C, Anderson A, Alexandrov K. The present and the future of protein biosensor engineering. Curr Opin Struct Biol 2022; 75:102424. [PMID: 35870398 DOI: 10.1016/j.sbi.2022.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Protein biosensors play increasingly important roles in cell and neurobiology and have the potential to revolutionise the way clinical and industrial analytics are performed. The gradual transition from multicomponent biosensors to fully integrated single chain allosteric biosensors has brought the field closer to commercial applications. We evaluate various approaches for converting constitutively active protein reporter domains into analyte operated switches. We discuss the paucity of the natural receptors that undergo conformational changes sufficiently large to control the activity of allosteric reporter domains. This problem can be overcome by constructing artificial versions of such receptors. The design path to such receptors involves the construction of Chemically Induced Dimerisation systems (CIDs) that can be configured to operate single and two-component biosensors.
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Affiliation(s)
- Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia; Australian Research Council Centre of Excellence in Synthetic Biology, Australian National University, Canberra, ACT 2601, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Alisha Anderson
- CSIRO Health & Biosecurity, Black Mountain, Canberra, ACT 2600, Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, Queensland University of Technology, Brisbane, QLD, 4001, Australia; Centre for Agriculture and the Bioeconomy, Centre for Genomics and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia; Australian Research Council Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
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8
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Koveal D, Rosen PC, Meyer DJ, Díaz-García CM, Wang Y, Cai LH, Chou PJ, Weitz DA, Yellen G. A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors. Nat Commun 2022; 13:2919. [PMID: 35614105 PMCID: PMC9133083 DOI: 10.1038/s41467-022-30685-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/11/2022] [Indexed: 12/30/2022] Open
Abstract
Genetically encoded fluorescent biosensors are powerful tools used to track chemical processes in intact biological systems. However, the development and optimization of biosensors remains a challenging and labor-intensive process, primarily due to technical limitations of methods for screening candidate biosensors. Here we describe a screening modality that combines droplet microfluidics and automated fluorescence imaging to provide an order of magnitude increase in screening throughput. Moreover, unlike current techniques that are limited to screening for a single biosensor feature at a time (e.g. brightness), our method enables evaluation of multiple features (e.g. contrast, affinity, specificity) in parallel. Because biosensor features can covary, this capability is essential for rapid optimization. We use this system to generate a high-performance biosensor for lactate that can be used to quantify intracellular lactate concentrations. This biosensor, named LiLac, constitutes a significant advance in metabolite sensing and demonstrates the power of our screening approach.
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Affiliation(s)
- Dorothy Koveal
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Paul C Rosen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dylan J Meyer
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Carlos Manlio Díaz-García
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yongcheng Wang
- Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
| | - Li-Heng Cai
- Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA, USA
| | - Peter J Chou
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Weitz
- Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
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9
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San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
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Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
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