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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. [PMID: 38822813 DOI: 10.1021/acssensors.4c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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Zhang Y, Kubiak AM, Bailey TS, Claessen L, Hittmeyer P, Dubois L, Theys J, Lambin P. Development of a CRISPR-Cas12a system for efficient genome engineering in clostridia. Microbiol Spectr 2023; 11:e0245923. [PMID: 37947521 PMCID: PMC10715149 DOI: 10.1128/spectrum.02459-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Continued efforts in developing the CRISPR-Cas systems will further enhance our understanding and utilization of Clostridium species. This study demonstrates the development and application of a genome-engineering tool in two Clostridium strains, Clostridium butyricum and Clostridium sporogenes, which have promising potential as probiotics and oncolytic agents. Particular attention was given to the folding of precursor crRNA and the role of this process in off-target DNA cleavage by Cas12a. The results provide the guidelines necessary for efficient genome engineering using this system in clostridia. Our findings not only expand our fundamental understanding of genome-engineering tools in clostridia but also improve this technology to allow use of its full potential in a plethora of biotechnological applications.
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Affiliation(s)
- Yanchao Zhang
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Aleksandra M. Kubiak
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Exomnis Biotech BV, Maastricht, The Netherlands
| | - Tom S. Bailey
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Luuk Claessen
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- LivingMed Biotech SRL, Liège, Belgium
| | - Philip Hittmeyer
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- LivingMed Biotech SRL, Liège, Belgium
| | - Ludwig Dubois
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Jan Theys
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Philippe Lambin
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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Maiti A, Buffalo CZ, Saurabh S, Montecinos-Franjola F, Hachey JS, Conlon WJ, Tran GN, Hassan B, Walters KJ, Drobizhev M, Moerner WE, Ghosh P, Matsuo H, Tsien RY, Lin JY, Rodriguez EA. Structural and photophysical characterization of the small ultra-red fluorescent protein. Nat Commun 2023; 14:4155. [PMID: 37438348 PMCID: PMC10338489 DOI: 10.1038/s41467-023-39776-9] [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: 06/27/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
The small Ultra-Red Fluorescent Protein (smURFP) represents a new class of fluorescent protein with exceptional photostability and brightness derived from allophycocyanin in a previous directed evolution. Here, we report the smURFP crystal structure to better understand properties and enable further engineering of improved variants. We compare this structure to the structures of allophycocyanin and smURFP mutants to identify the structural origins of the molecular brightness. We then use a structure-guided approach to develop monomeric smURFP variants that fluoresce with phycocyanobilin but not biliverdin. Furthermore, we measure smURFP photophysical properties necessary for advanced imaging modalities, such as those relevant for two-photon, fluorescence lifetime, and single-molecule imaging. We observe that smURFP has the largest two-photon cross-section measured for a fluorescent protein, and that it produces more photons than organic dyes. Altogether, this study expands our understanding of the smURFP, which will inform future engineering toward optimal FPs compatible with whole organism studies.
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Affiliation(s)
- Atanu Maiti
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Cosmo Z Buffalo
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Saumya Saurabh
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | | | - Justin S Hachey
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - William J Conlon
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Geraldine N Tran
- Department of Radiology, Boston University, Boston, MA, 02118, USA
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Partho Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroshi Matsuo
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Roger Y Tsien
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, La Jolla, CA, 92093, USA
| | - John Y Lin
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, 7000, Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
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Trashi I, Durbacz MZ, Trashi O, Wijesundara YH, Ehrman RN, Chiev AC, Darwin CB, Herbert FC, Gadhvi J, De Nisco NJ, Nielsen SO, Gassensmith JJ. Self-assembly of a fluorescent virus-like particle for imaging in tissues with high autofluorescence. J Mater Chem B 2023; 11:4445-4452. [PMID: 37144595 DOI: 10.1039/d3tb00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Virus-like particles (VLPs) are engineered nanoparticles that mimic the properties of viruses-like high tolerance to heat and proteases-but lack a viral genome, making them non-infectious. They are easily modified chemically and genetically, making them useful in drug delivery, enhancing vaccine efficacy, gene delivery, and cancer immunotherapy. One such VLP is Qβ, which has an affinity towards an RNA hairpin structure found in its viral RNA that drives the self-assembly of the capsid. It is possible to usurp the native way infectious Qβ self-assembles to encapsidate its RNA to place enzymes inside the VLP's lumen as a protease-resistant cage. Further, using RNA templates that mimic the natural self-assembly of the native capsid, fluorescent proteins (FPs) have been placed inside VLPs in a "one pot" expression system. Autofluorescence in tissues can lead to misinterpretation of results and unreliable science, so we created a single-pot expression system that uses the fluorescent protein smURFP, which avoids autofluorescence and has spectral properties compatible with standard commercial filter sets on confocal microscopes. In this work, we were able to simplify the existing "one-pot" expression system while creating high-yielding fluorescent VLP nanoparticles that could easily be imaged inside lung epithelial tissue.
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Affiliation(s)
- Ikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Mateusz Z Durbacz
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Orikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Ryanne N Ehrman
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Alyssa C Chiev
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Cary B Darwin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Jashkaran Gadhvi
- Department of Biological Science, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Nicole J De Nisco
- Department of Biological Science, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Steven O Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas 75080, USA
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5
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Sokolov P, Nifontova G, Samokhvalov P, Karaulov A, Sukhanova A, Nabiev I. Nontoxic Fluorescent Nanoprobes for Multiplexed Detection and 3D Imaging of Tumor Markers in Breast Cancer. Pharmaceutics 2023; 15:pharmaceutics15030946. [PMID: 36986807 PMCID: PMC10052755 DOI: 10.3390/pharmaceutics15030946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Multiplexed fluorescent immunohistochemical analysis of breast cancer (BC) markers and high-resolution 3D immunofluorescence imaging of the tumor and its microenvironment not only facilitate making the disease prognosis and selecting effective anticancer therapy (including photodynamic therapy), but also provides information on signaling and metabolic mechanisms of carcinogenesis and helps in the search for new therapeutic targets and drugs. The characteristics of imaging nanoprobe efficiency, such as sensitivity, target affinity, depth of tissue penetration, and photostability, are determined by the properties of their components, fluorophores and capture molecules, and by the method of their conjugation. Regarding individual nanoprobe components, fluorescent nanocrystals (NCs) are widely used for optical imaging in vitro and in vivo, and single-domain antibodies (sdAbs) are well established as highly specific capture molecules in diagnostic and therapeutic applications. Moreover, the technologies of obtaining functionally active sdAb–NC conjugates with the highest possible avidity, with all sdAb molecules bound to the NC in a strictly oriented manner, provide 3D-imaging nanoprobes with strong comparative advantages. This review is aimed at highlighting the importance of an integrated approach to BC diagnosis, including the detection of biomarkers of the tumor and its microenvironment, as well as the need for their quantitative profiling and imaging of their mutual location, using advanced approaches to 3D detection in thick tissue sections. The existing approaches to 3D imaging of tumors and their microenvironment using fluorescent NCs are described, and the main comparative advantages and disadvantages of nontoxic fluorescent sdAb–NC conjugates as nanoprobes for multiplexed detection and 3D imaging of BC markers are discussed.
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Affiliation(s)
- Pavel Sokolov
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115522 Moscow, Russia
| | - Galina Nifontova
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Pavel Samokhvalov
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115522 Moscow, Russia
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia
| | - Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Igor Nabiev
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115522 Moscow, Russia
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne, 51100 Reims, France
- Department of Clinical Immunology and Allergology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia
- Correspondence:
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6
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Wu T, Kumar M, Zhang J, Zhao S, Drobizhev M, McCollum M, Anderson CT, Wang Y, Pokorny A, Tian X, Zhang Y, Tzounopoulos T, Ai HW. A genetically encoded far-red fluorescent indicator for imaging synaptically released Zn 2. SCIENCE ADVANCES 2023; 9:eadd2058. [PMID: 36857451 PMCID: PMC9977179 DOI: 10.1126/sciadv.add2058] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Synaptic zinc ion (Zn2+) has emerged as a key neuromodulator in the brain. However, the lack of research tools for directly tracking synaptic Zn2+ in the brain of awake animals hinders our rigorous understanding of the physiological and pathological roles of synaptic Zn2+. In this study, we developed a genetically encoded far-red fluorescent indicator for monitoring synaptic Zn2+ dynamics in the nervous system. Our engineered far-red fluorescent indicator for synaptic Zn2+ (FRISZ) displayed a substantial Zn2+-specific turn-on response and low-micromolar affinity. We genetically anchored FRISZ to the mammalian extracellular membrane via a transmembrane (TM) ⍺ helix and characterized the resultant FRISZ-TM construct at the mammalian cell surface. We used FRISZ-TM to image synaptic Zn2+ in the auditory cortex in acute brain slices and awake mice in response to electric and sound stimuli, respectively. Thus, this study establishes a technology for studying the roles of synaptic Zn2+ in the nervous system.
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Affiliation(s)
- Tianchen Wu
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Manoj Kumar
- Department of Otolaryngology, Pittsburgh Hearing Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jing Zhang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Shengyu Zhao
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717-384, USA
| | - Mason McCollum
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA
| | - Charles T. Anderson
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA
| | - Ying Wang
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Xiaodong Tian
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yiyu Zhang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Thanos Tzounopoulos
- Department of Otolaryngology, Pittsburgh Hearing Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- The UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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Van Thillo T, Van Deuren V, Dedecker P. Smart genetically-encoded biosensors for the chemical monitoring of living systems. Chem Commun (Camb) 2023; 59:520-534. [PMID: 36519509 DOI: 10.1039/d2cc05363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetically-encoded biosensors provide the all-optical and non-invasive visualization of dynamic biochemical events within living systems, which has allowed the discovery of profound new insights. Twenty-five years of biosensor development has steadily improved their performance and has provided us with an ever increasing biosensor repertoire. In this feature article, we present recent advances made in biosensor development and provide a perspective on the future direction of the field.
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Affiliation(s)
- Toon Van Thillo
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Vincent Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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8
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Mattson S, Tran GN, Rodriguez EA. Directed Evolution of Fluorescent Proteins in Bacteria. Methods Mol Biol 2023; 2564:75-97. [PMID: 36107338 DOI: 10.1007/978-1-0716-2667-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Directed evolution has revolutionized the way scientists create new biomolecules not found in nature. Error-prone polymerase chain reaction (PCR) introduces random mutations and was used to evolve jellyfish and coral fluorescent proteins in bacteria. We describe a novel method for the directed evolution of a far-red fluorescent protein in E. coli. The new method used genes to produce fluorophores inside E. coli and allowed changing the native fluorophore, phycocyanobilin, for a second small-molecule fluorophore, biliverdin. The directed evolution blueshifted the fluorescence, which enhanced the quantum yield to produce a brighter fluorescent protein. Finally, the evolution selected fluorescent proteins that expressed in large quantities in E. coli. The evolved fluorescent protein was named the small ultra-red fluorescent protein (smURFP) and was biophysically as bright as the enhanced green fluorescent protein (EGFP). This chapter describes the materials and methods used to evolve a far-red fluorescent protein in bacteria. While the focus is a fluorescent protein, the protocol is adaptable for the evolution of other biomolecules in bacteria when using a proper selection strategy.
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Affiliation(s)
- Sara Mattson
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Geraldine N Tran
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, USA.
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Boitet M, Eun H, Lee T, Kim J, Grailhe R. Non-invasive In Vivo Brain Astrogenesis and Astrogliosis Quantification Using a Far-red E2-Crimson Transgenic Reporter Mouse. Mol Neurobiol 2022; 59:6740-6753. [PMID: 36001234 DOI: 10.1007/s12035-022-02997-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
Abstract
Despite the adaptation of major clinical imaging modalities for small animals, optical bioluminescence imaging technology is the main approach readily reporting gene activity. Yet, in vivo bioluminescence monitoring requires the administration and diffusion of a substrate to the tissues of interest, resulting in experimental variability, high reagent cost, long acquisition time, and stress to the animal. In our study, we avoid such issues upon generating a new transgenic mouse (GFAP-E2crimson) expressing the far-red fluorescent protein E2-crimson under the control of the glial fibrillary acidic protein (GFAP) promoter. Using microscopy, we validated the selective expression of the reporter in the astrocyte cell population and by non-invasive in vivo fluorescence imaging its detection through the scalps and skulls of live animals. In addition, we performed a longitudinal study validating by in vivo imaging that the E2-crimson fluorescence signal is up-regulated, in pups during astrogenesis and in adult mice during astrogliosis upon kainic acid administration. Furthermore, upon crossing GFAP-E2crimson transgenic with 5XFAD Alzheimer's disease mice model, we were able to quantify the chronic inflammation triggered by amyloid deposit and aging over 18 months. As many diseases and conditions can trigger neuroinflammation, we believe that the GFAP-E2crimson reporter mice model delivers tremendous value for the non-invasive quantification of astrogliosis responses in living animals.
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Affiliation(s)
- Maylis Boitet
- Technology Development Platform, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
- Department of Biological Chemistry, IPK Campus, Korea University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Hyeju Eun
- Technology Development Platform, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
| | - Taekwan Lee
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jiho Kim
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea.
- Department of Biological Chemistry, IPK Campus, Korea University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, 34113, Republic of Korea.
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10
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Almogbil HH, Montecinos-Franjola F, Daszynski C, Conlon WJ, Hachey JS, Corazza G, Rodriguez EA, Zderic V. Therapeutic Ultrasound for Topical Corneal Delivery of Macromolecules. Transl Vis Sci Technol 2022; 11:23. [PMID: 35998058 PMCID: PMC9424970 DOI: 10.1167/tvst.11.8.23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose The objective of this study was to utilize therapeutic ultrasound in enhancing delivery of topical macromolecules into the cornea. Methods Rabbit corneas were dissected and placed in a diffusion cell with a small ultra-red fluorescent protein (smURFP; molecular weight of 32,000 Da) as a macromolecule solution. The corneas were treated with continuous ultrasound application at frequencies of 400 or 600 kHz and intensities of 0.8 to 1.0 W/cm2 for 5 minutes, or sham-treated. Fluorescence imaging of the cornea sections was used to observe the delivery of macromolecules into individual epithelial cells. Spectrophotometric analysis at smURFP maximal absorbance of 640 nm was done to determine the presence of macromolecules in the receiver compartment. Safety of ultrasound application was studied through histology analysis. Results Ultrasound-treated corneas showed smURFP delivery into epithelial cells by fluorescence in the cytoplasm, whereas sham-treated corneas lacked any appreciable fluorescence in the individual cells. The sham group showed 0% of subcellular penetration, whereas the 400 kHz ultrasound-treated group and 600 kHz ultrasound-treated group showed 31% and 57% of subcellular penetration, respectively. Spectrophotometry measurements indicated negligible presence of smURFP macromolecules in the receiver compartment solution in both the sham and ultrasound treatment groups, and these macromolecules did not cross the entire depth of the cornea. Histological studies showed no significant corneal damage due to ultrasound application. Conclusions Therapeutic ultrasound application was shown to increase the delivery of smURFP macromolecules into the cornea. Translational Relevance Our study offers a clinical potential for a minimally invasive macromolecular treatment of corneal diseases.
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Affiliation(s)
- Hanaa H. Almogbil
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | | | - Camille Daszynski
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - William J. Conlon
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Justin S. Hachey
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Giavanna Corazza
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - Erik A. Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Vesna Zderic
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
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11
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Liu F, Hu H, Deng M, Xiang Z, Guo Y, Guan X, Li D, Hu Q, Lei W, Peng H, Chu J. A Bright Monomeric Near-Infrared Fluorescent Protein with an Excitation Peak at 633 nm for Labeling Cellular Protein and Reporting Protein-Protein Interaction. ACS Sens 2022; 7:1855-1866. [PMID: 35775925 DOI: 10.1021/acssensors.2c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bright monomeric near-infrared fluorescent proteins (NIR-FPs) are useful as markers for labeling proteins and cells and as sensors for reporting molecular activities in living cells and organisms. However, current monomeric NIR-FPs are dim under excitation with common 633/635/640 nm lasers, limiting their broad use in cellular/subcellular level imaging. Here, we report a bright monomeric NIR-FP with maximum excitation at 633 nm, named mIFP663, engineered from Xanthomonas campestris pv Campestris phytochrome (XccBphP). mIFP663 has high molecular brightness with a large extinction coefficient (86,600 M-1 cm-1) and a decent quantum yield (19.4%), and high cellular brightness that is 3-6 times greater than those of spectrally similar NIR-FPs in HEK293T cells in the presence of exogenous BV. Moreover, we demonstrate that mIFP663 is able to label critical cellular and viral proteins without perturbing subcellular localization and virus replication, respectively. Finally, with mIFP663, we engineer improved bimolecular fluorescence complementation (BiFC) and new bioluminescent resonance energy transfer (BRET) systems to detect protein-protein interactions in living cells.
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Affiliation(s)
- Feng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & Center for Biomedical Optics and Molecular Imaging & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huimin Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengying Deng
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & Center for Biomedical Optics and Molecular Imaging & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zongqin Xiang
- Department of Neurosurgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, China
| | - Yuting Guo
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinmeng Guan
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & Center for Biomedical Optics and Molecular Imaging & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinxue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.,Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, United Kingdom
| | - Wenliang Lei
- Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510630, China
| | - Hongjuan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & Center for Biomedical Optics and Molecular Imaging & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
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12
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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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13
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Fujii H, Bito H. Deciphering Ca2+-controlled biochemical computation governing neural circuit dynamics via multiplex imaging. Neurosci Res 2022; 179:79-90. [DOI: 10.1016/j.neures.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/25/2022]
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14
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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15
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Wu T, Pang Y, Ai HW. Circularly Permuted Far-Red Fluorescent Proteins. BIOSENSORS 2021; 11:438. [PMID: 34821654 PMCID: PMC8615523 DOI: 10.3390/bios11110438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
The color palette of genetically encoded fluorescent protein indicators (GEFPIs) has expanded rapidly in recent years. GEFPIs with excitation and emission within the "optical window" above 600 nm are expected to be superior in many aspects, such as enhanced tissue penetration, reduced autofluorescence and scattering, and lower phototoxicity. Circular permutation of fluorescent proteins (FPs) is often the first step in the process of developing single-FP-based GEFPIs. This study explored the tolerance of two far-red FPs, mMaroon1 and mCarmine, towards circular permutation. Several initial constructs were built according to previously reported circularly permuted topologies for other FP analogs. Mutagenesis was then performed on these constructs and screened for fluorescent variants. As a result, five circularly permuted far-red FPs (cpFrFPs) with excitation and emission maxima longer than 600 nm were identified. Some displayed appreciable brightness and efficient chromophore maturation. These cpFrFPs variants could be intriguing starting points to further engineer far-red GEFPIs for in vivo tissue imaging.
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Affiliation(s)
- Tianchen Wu
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
| | - Yu Pang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
- The UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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16
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Machado JH, Ting R, Lin JY, Rodriguez EA. A self-labeling protein based on the small ultra-red fluorescent protein, smURFP. RSC Chem Biol 2021; 2:1221-1226. [PMID: 34458834 PMCID: PMC8341759 DOI: 10.1039/d1cb00127b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 12/25/2022] Open
Abstract
Self-labeling proteins have revolutionized super-resolution and sensor imaging. Tags recognize a bioorthogonal substrate for covalent attachment. We show the small Ultra-Red Fluorescent Protein (smURFP) is a self-labeling protein. The substrate is fluorogenic, fluoresces when attached, and quenches fluorescent cargo. The smURFP-tag has novel properties for tool development.
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Affiliation(s)
- John-Hanson Machado
- Department of Chemistry, The George Washington University Washington DC 20052 USA
| | - Richard Ting
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine New York NY 10065 USA
- Antelope Surgical, Biolabs@NYULangone New York NY 10014 USA
| | - John Y Lin
- Tasmanian School of Medicine, University of Tasmania Hobart Tasmania 7000 Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University Washington DC 20052 USA
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