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Lee J, Campillo B, Hamidian S, Liu Z, Shorey M, St-Pierre F. Automating the High-Throughput Screening of Protein-Based Optical Indicators and Actuators. Biochemistry 2023; 62:169-177. [PMID: 36315460 PMCID: PMC9852035 DOI: 10.1021/acs.biochem.2c00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Over the last 25 years, protein engineers have developed an impressive collection of optical tools to interface with biological systems: indicators to eavesdrop on cellular activity and actuators to poke and prod native processes. To reach the performance level required for their downstream applications, protein-based tools are usually sculpted by iterative rounds of mutagenesis. In each round, libraries of variants are made and evaluated, and the most promising hits are then retrieved, sequenced, and further characterized. Early efforts to engineer protein-based optical tools were largely manual, suffering from low throughput, human error, and tedium. Here, we describe approaches to automating the screening of libraries generated as colonies on agar, multiwell plates, and pooled populations of single-cell variants. We also briefly discuss emerging approaches for screening, including cell-free systems and machine learning.
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Affiliation(s)
- Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Beatriz Campillo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaminta Hamidian
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Matthew Shorey
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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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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Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B 2022; 126:735-750. [DOI: 10.1021/acs.jpcb.1c05629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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Drobizhev M, Molina RS, Franklin J. Multiphoton Bleaching of Red Fluorescent Proteins and the Ways to Reduce It. Int J Mol Sci 2022; 23:770. [PMID: 35054953 PMCID: PMC8775990 DOI: 10.3390/ijms23020770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/16/2022] Open
Abstract
Red fluorescent proteins and biosensors built upon them are potentially beneficial for two-photon laser microscopy (TPLM) because they can image deeper layers of tissue, compared to green fluorescent proteins. However, some publications report on their very fast photobleaching, especially upon excitation at 750-800 nm. Here we study the multiphoton bleaching properties of mCherry, mPlum, tdTomato, and jREX-GECO1, measuring power dependences of photobleaching rates K at different excitation wavelengths across the whole two-photon absorption spectrum. Although all these proteins contain the chromophore with the same chemical structure, the mechanisms of their multiphoton bleaching are different. The number of photons required to initiate a photochemical reaction varies, depending on wavelength and power, from 2 (all four proteins) to 3 (jREX-GECO1) to 4 (mCherry, mPlum, tdTomato), and even up to 8 (tdTomato). We found that at sufficiently low excitation power P, the rate K often follows a quadratic power dependence, that turns into higher order dependence (K~Pα with α > 2) when the power surpasses a particular threshold P*. An optimum intensity for TPLM is close to the P*, because it provides the highest signal-to-background ratio and any further reduction of laser intensity would not improve the fluorescence/bleaching rate ratio. Additionally, one should avoid using wavelengths shorter than a particular threshold to avoid fast bleaching due to multiphoton ionization.
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Affiliation(s)
- Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA;
| | - Rosana S. Molina
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA;
| | - Jacob Franklin
- Vidrio Technologies LLC, 19955 Highland Vista Drive Suite 150, Ashburn, VA 20147, USA;
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