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Jimbo M, Otake M, Amano H, Yasumoto K, Watabe S, Okada D, Kumagai H. Characterization of recombinant photoconverting green fluorescent Akanes. J Biochem 2023; 175:25-34. [PMID: 37812399 DOI: 10.1093/jb/mvad078] [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: 04/27/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
Akanes are fluorescent proteins that have several fluorescence maxima. In this report, Akane1 and Akane3 from Scleronephthya gracillima were selected, successfully overexpressed in Escherichia coli and purified by affinity chromatography. Fluorescence spectra of the recombinant Akanes matured in darkness, or ambient light were found to have several fluorescence peaks. SDS-PAGE analysis revealed that Akanes matured in ambient light have two fragments. MS/MS analysis of Akanes digested with trypsin showed that the cleavage site is the same as observed for the photoconvertible fluorescent protein Kaede. The differences between the calculated masses from the amino acid sequence of Akane1 and the measured masses of Akane1 fragments obtained under ambient light coincided with those of Kaede. In contrast, a mass difference between the measured N-terminal Akane3 fragment and the calculated mass indicated that Akane3 is modified in the N-terminal region. These results indicate that numerous peaks in the fluorescent spectra of Akanes partly arise from isoproteins of Akanes and photoconversion. Photoconversion of Akane1 caused a fluorescence change from green to red, which was also observed for Akane3; however, the fluorescent intensity decreased dramatically when compared with that of Akane3.
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Affiliation(s)
- Mitsuru Jimbo
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Mayumi Otake
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Haruna Amano
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Daisuke Okada
- School of Medicine, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Hiroshi Kumagai
- School of Allied Health Sciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
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2
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Sartor A, Dahlberg PD, Perez D, Moerner WE. Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms. J Phys Chem B 2023; 127:2690-2700. [PMID: 36943356 PMCID: PMC10069424 DOI: 10.1021/acs.jpcb.2c08995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/01/2023] [Indexed: 03/23/2023]
Abstract
Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.
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Affiliation(s)
- Annina
M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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3
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Tosheva KL, Yuan Y, Matos Pereira P, Culley S, Henriques R. Between life and death: strategies to reduce phototoxicity in super-resolution microscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:163001. [PMID: 33994582 PMCID: PMC8114953 DOI: 10.1088/1361-6463/ab6b95] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 01/14/2020] [Indexed: 05/23/2023]
Abstract
Super-resolution microscopy (SRM) enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for live-cell observations, particularly for extended periods of time. Here, we give an overview of new developments in hardware, software and probe chemistry aiming to reduce phototoxicity. Additionally, we discuss how the choice of biological model and sample environment impacts the capacity for live-cell observations.
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Affiliation(s)
- Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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4
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Krueger TD, Tang L, Zhu L, Breen IL, Wachter RM, Fang C. Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein. Angew Chem Int Ed Engl 2020; 59:1644-1652. [PMID: 31692171 DOI: 10.1002/anie.201911379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Indexed: 01/13/2023]
Abstract
The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light-induced processes. We implemented time-resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP-like protein LEA, involving semi-trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual-illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge-H bending motions enables rational design of functional proteins. With the improved H-bonding network and structural motions, the photoexcited chromophore could increase the photoswitching-aided photoconversion while reducing trapped species.
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Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| | - Isabella L Breen
- School of Molecular Sciences, Center for Bioenergy and Photosynthesis, Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Rebekka M Wachter
- School of Molecular Sciences, Center for Bioenergy and Photosynthesis, Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
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5
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Krueger TD, Tang L, Zhu L, Breen IL, Wachter RM, Fang C. Dual Illumination Enhances Transformation of an Engineered Green‐to‐Red Photoconvertible Fluorescent Protein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Taylor D. Krueger
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| | - Longteng Tang
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| | - Liangdong Zhu
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| | - Isabella L. Breen
- School of Molecular Sciences Center for Bioenergy and Photosynthesis Biodesign Center for Applied Structural Discovery Arizona State University Tempe AZ 85287 USA
| | - Rebekka M. Wachter
- School of Molecular Sciences Center for Bioenergy and Photosynthesis Biodesign Center for Applied Structural Discovery Arizona State University Tempe AZ 85287 USA
| | - Chong Fang
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
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Welling M, Mohr MA, Ponti A, Rullan Sabater L, Boni A, Kawamura YK, Liberali P, Peters AH, Pelczar P, Pantazis P. Primed Track, high-fidelity lineage tracing in mouse pre-implantation embryos using primed conversion of photoconvertible proteins. eLife 2019; 8:44491. [PMID: 30663981 PMCID: PMC6340703 DOI: 10.7554/elife.44491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/24/2018] [Indexed: 11/13/2022] Open
Abstract
Accurate lineage reconstruction of mammalian pre-implantation development is essential for inferring the earliest cell fate decisions. Lineage tracing using global fluorescence labeling techniques is complicated by increasing cell density and rapid embryo rotation, which hampers automatic alignment and accurate cell tracking of obtained four-dimensional imaging data sets. Here, we exploit the advantageous properties of primed convertible fluorescent proteins (pr-pcFPs) to simultaneously visualize the global green and the photoconverted red population in order to minimize tracking uncertainties over prolonged time windows. Confined primed conversion of H2B-pr-mEosFP-labeled nuclei combined with light-sheet imaging greatly facilitates segmentation, classification, and tracking of individual nuclei from the 4-cell stage up to the blastocyst. Using green and red labels as fiducial markers, we computationally correct for rotational and translational drift, reduce overall data size, and accomplish high-fidelity lineage tracing even for increased imaging time intervals – addressing major concerns in the field of volumetric embryo imaging. A mouse embryo starts with one cell, which divides to create identical daughters that quickly start to multiply. Within three to four days, certain cells begin to specialize and take on specific roles. Scientists want to track these early events to understand how they give rise to an individual formed of huge numbers of cells organized in specialized tissues. To do so, researchers genetically manipulate embryos so that each cell produces fluorescent molecules that ‘glow’ under light. These embryos are grown inside a special microscope for several days. Images are taken regularly and then processed by specialized software that automatically tracks the fluorescent cells and their daughters over time. This helps reconstruct the history of each cell, and which structures they give rise to. However, many embryos move and turn around between images, and so software packages often lose track of which cell was which. Taking images more frequently is not possible because each imaging event exposes the embryo to light, which can damage its fragile cells. To address this problem, Welling, Mohr et al. made embryonic cells produce a special fluorescent marker, which is normally green but can be converted to red. Then, a technique known as primed conversion was used so that only one cell in a four-cell embryo would glow red. Welling, Mohr et al. designed a piece of software, baptized ‘primed Track’, that can use this red cell (and its daughters) to reorient the embryo during image analysis and reliably identify and match any mother cell to its daughters. The new approach means the experiments require fewer imaging events, but also fewer embryos because even the ones that move a lot can be studied. This should help scientists look into how early life processes give rise to specialized cells, and even explore the fate of cells in other tissues.
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Affiliation(s)
- Maaike Welling
- Department for Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland.,Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Manuel Alexander Mohr
- Department for Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Aaron Ponti
- Department for Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
| | - Lluc Rullan Sabater
- Department for Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
| | - Andrea Boni
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Yumiko K Kawamura
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Antoine Hfm Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Pawel Pelczar
- Center for Transgenic Models (CTM), University of Basel, Basel, Switzerland
| | - Periklis Pantazis
- Department for Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland.,Department of Bioengineering, Imperial College London, London, United Kingdom
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