1
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Vazquez ND, Crupkin AC, Chierichetti MA, Acuña FH, Miglioranza KSB. Integrated biomarker responses in wild populations of the intertidal sea anemone Bunodosoma zamponii living under different anthropogenic pressures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:26036-26051. [PMID: 38491242 DOI: 10.1007/s11356-024-32926-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Bunodosoma zamponii is the most abundant anemone in Mar del Plata (Buenos Aires, Argentina). Given that the presence of persistent organic pollutants (organochlorine pesticides and PCBs) and the organophosphate pesticide chlorpyrifos has recently been reported in this species, two wild populations living under different anthropogenic pressures were studied and compared regarding basic aspects of their ecology and physiological response to oxidative stress. A population from an impacted site (Las Delicias, LD) and another from a reference site (Punta Cantera, PC) were monitored seasonally (spring, summer, autumn, and winter), for one year. Anemones from PC were larger and more abundant than those from LD for most sampling periods. During winter, glutathione-S-transferase and catalase activities were higher in LD. Moreover, protein content and antioxidant defenses were higher in anemones from PC during winter as well. Taking into account their ecology (size and abundance) and biomarker responses, the population from PC was comparatively healthier. Furthermore, such differences are in agreement with recent studies indicating a higher concentration of pollutants in anemones from LD (specially during the winter sampling). In this sense, considering that B. zamponii can bioaccumulate the aforementioned pollutants, its resilience to their presence, and the fact that biomarker response differed between sites, this species can be regarded as a proper sentinel species of environmental pollution. Overall, this anemone seems to be a good bioindicator to be considered in future biomonitoring and ecotoxicological studies.
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Affiliation(s)
- Nicolas D Vazquez
- Institute of Marine and Coastal Research, National Scientific and Technological Research Council, Mar del Plata, Buenos Aires, Argentina.
- Laboratory of Ecotoxicology and Environmental Contamination, Faculty of Exact and Natural Sciences, National University of Mar del Plata, Mar del Plata, Buenos Aires, Argentina.
- Laboratory of Cnidarian Biology, Faculty of Exact and Natural Sciences, National University of Mar del Plata, Mar del Plata, Buenos Aires, Argentina.
| | - Andrea C Crupkin
- Institute of Marine and Coastal Research, National Scientific and Technological Research Council, Mar del Plata, Buenos Aires, Argentina
- Laboratory of Ecotoxicology, Faculty of Exact and Natural Sciences, National University of Mar del Plata, Mar del Plata, Buenos Aires, Argentina
- Scientific Research Commission of the Province of Buenos Aires, Buenos Aires, Argentina
| | - Melisa A Chierichetti
- Institute of Marine and Coastal Research, National Scientific and Technological Research Council, Mar del Plata, Buenos Aires, Argentina
- Laboratory of Ecotoxicology and Environmental Contamination, Faculty of Exact and Natural Sciences, National University of Mar del Plata, Mar del Plata, Buenos Aires, Argentina
| | - Fabián H Acuña
- Institute of Marine and Coastal Research, National Scientific and Technological Research Council, Mar del Plata, Buenos Aires, Argentina
- Laboratory of Cnidarian Biology, Faculty of Exact and Natural Sciences, National University of Mar del Plata, Mar del Plata, Buenos Aires, Argentina
- Coiba Research Station (Coiba-AIP), Panama, Republic of Panama
| | - Karina S B Miglioranza
- Institute of Marine and Coastal Research, National Scientific and Technological Research Council, Mar del Plata, Buenos Aires, Argentina
- Laboratory of Ecotoxicology and Environmental Contamination, Faculty of Exact and Natural Sciences, National University of Mar del Plata, Mar del Plata, Buenos Aires, Argentina
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2
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Poding LH, Jägers P, Herlitze S, Huhn M. Diversity and function of fluorescent molecules in marine animals. Biol Rev Camb Philos Soc 2024. [PMID: 38468189 DOI: 10.1111/brv.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Fluorescence in marine animals has mainly been studied in Cnidaria but is found in many different phyla such as Annelida, Crustacea, Mollusca, and Chordata. While many fluorescent proteins and molecules have been identified, very little information is available about the biological functions of fluorescence. In this review, we focus on describing the occurrence of fluorescence in marine animals and the behavioural and physiological functions of fluorescent molecules based on experimental approaches. These biological functions of fluorescence range from prey and symbiont attraction, photoprotection, photoenhancement, stress mitigation, mimicry, and aposematism to inter- and intraspecific communication. We provide a comprehensive list of marine taxa that utilise fluorescence, including demonstrated effects on behavioural or physiological responses. We describe the numerous known functions of fluorescence in anthozoans and their underlying molecular mechanisms. We also highlight that other marine taxa should be studied regarding the functions of fluorescence. We suggest that an increase in research effort in this field could contribute to understanding the capacity of marine animals to respond to negative effects of climate change, such as rising sea temperatures and increasing intensities of solar irradiation.
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Affiliation(s)
- Lars H Poding
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Peter Jägers
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Mareike Huhn
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
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3
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Zhu YH, Liu XX, Fang Q, Liu XY, Fang WH, Cui G. Multiple Photoisomerization Pathways of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein: Insights from Quantum Mechanics/Molecular Mechanics Simulations. J Phys Chem Lett 2023; 14:2588-2598. [PMID: 36881005 DOI: 10.1021/acs.jpclett.3c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Herein, we have employed a combined CASPT2//CASSCF approach within the quantum mechanics/molecular mechanics (QM/MM) framework to explore the early time photoisomerization of rsEGFP2 starting from its two OFF trans states, i.e., Trans1 and Trans2. The results show similar vertical excitation energies to the S1 state in their Franck-Condon regions. Considering the clockwise and counterclockwise rotations of the C11-C9 bond, four pairs of the S1 excited-state minima and low-lying S1/S0 conical intersections were optimized, based on which we determined four S1 photoisomerization paths that are essentially barrierless to the relevant S1/S0 conical intersections leading to efficient excited-state deactivation to the S0 state. Most importantly, our work first identified multiple photoisomerization and excited-state decay paths, which must be seriously considered in the future. This work not only sheds significant light on the primary trans-cis photoisomerization of rsEGFP2 but also aids in the understanding of the microscopic mechanism of GFP-like RSFPs and the design of novel GFP-like fluorescent proteins.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xin-Xin Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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4
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Application of Genetically Encoded Photoconvertible Protein SAASoti for the Study of Enzyme Activity in a Single Live Cell by Fluorescence Correlation Microscopy. MATERIALS 2022; 15:ma15144962. [PMID: 35888428 PMCID: PMC9316514 DOI: 10.3390/ma15144962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/07/2022]
Abstract
Fluorescent Correlation Spectroscopy (FCS) allows us to determine interactions of labeled proteins or changes in the oligomeric state. The FCS method needs a low amount of fluorescent dye, near nanomolar concentrations. To control the amount of fluorescent dye, we used new photoconvertible FP SAASoti. This work is devoted to the proof of principle of using photoconvertible proteins to measure caspase enzymatic activity in a single live cell. The advantage of this approach is that partial photoconversion of the FP makes FCS measurements possible when studying enzymatic reactions. To investigate the process, in vivo we used HeLa cell line expressing the engineered FRET sensor, SAASoti-23-KFP. This FRET sensor has a cleavable (DEVD) sequence in the linker between two FPs for the detection of one of the key enzymes of apoptosis, caspase-3. Caspase-3 activity was detected by registering the increase in the fluorescent lifetimes of the sensor, whereas the diffusion coefficient of SAASoti decreased. This can be explained by an increase in the total cell viscosity during apoptosis. We can suppose that in the moment of detectible caspase-3 activity, cell structure already has crucial changes in viscosity.
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5
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Tang L, Fang C. Photoswitchable Fluorescent Proteins: Mechanisms on Ultrafast Timescales. Int J Mol Sci 2022; 23:ijms23126459. [PMID: 35742900 PMCID: PMC9223536 DOI: 10.3390/ijms23126459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
The advancement of super-resolution imaging (SRI) relies on fluorescent proteins with novel photochromic properties. Using light, the reversibly switchable fluorescent proteins (RSFPs) can be converted between bright and dark states for many photocycles and their emergence has inspired the invention of advanced SRI techniques. The general photoswitching mechanism involves the chromophore cis-trans isomerization and proton transfer for negative and positive RSFPs and hydration-dehydration for decoupled RSFPs. However, a detailed understanding of these processes on ultrafast timescales (femtosecond to millisecond) is lacking, which fundamentally hinders the further development of RSFPs. In this review, we summarize the current progress of utilizing various ultrafast electronic and vibrational spectroscopies, and time-resolved crystallography in investigating the on/off photoswitching pathways of RSFPs. We show that significant insights have been gained for some well-studied proteins, but the real-time "action" details regarding the bidirectional cis-trans isomerization, proton transfer, and intermediate states remain unclear for most systems, and many other relevant proteins have not been studied yet. We expect this review to lay the foundation and inspire more ultrafast studies on existing and future engineered RSFPs. The gained mechanistic insights will accelerate the rational development of RSFPs with enhanced two-way switching rate and efficiency, better photostability, higher brightness, and redder emission colors.
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6
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First biphotochromic fluorescent protein moxSAASoti stabilized for oxidizing environment. Sci Rep 2022; 12:7862. [PMID: 35551209 PMCID: PMC9098843 DOI: 10.1038/s41598-022-11249-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
Biphotochromic proteins simultaneously possess reversible photoswitching (on-to-off) and irreversible photoconversion (green-to-red). High photochemical reactivity of cysteine residues is one of the reasons for the development of "mox"-monomeric and oxidation resistant proteins. Based on site-saturated simultaneous two-point C105 and C117 mutagenesis, we chose C21N/C71G/C105G/C117T/C175A as the moxSAASoti variant. Since its on-to-off photoswitching rate is higher, off-to-on recovery is more complete and photoconversion rates are higher than those of mSAASoti. We analyzed the conformational behavior of the F177 side chain by classical MD simulations. The conformational flexibility of the F177 side chain is mainly responsible for the off-to-on conversion rate changes and can be further utilized as a measure of the conversion rate. Point mutations in mSAASoti mainly affect the pKa values of the red form and off-to-on switching. We demonstrate that the microscopic measure of the observed pKa value is the C-O bond length in the phenyl fragment of the neutral chromophore. According to molecular dynamics simulations with QM/MM potentials, larger C-O bond lengths are found for proteins with larger pKa. This feature can be utilized for prediction of the pKa values of red fluorescent proteins.
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7
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Zhai L, Nakashima R, Shinoda H, Ike Y, Matsuda T, Nagai T. Structure‐based analysis and evolution of a monomerized red‐colored chromoprotein from the
Olindias formosa
jellyfish. Protein Sci 2022; 31:e4285. [PMID: 35481635 PMCID: PMC8994484 DOI: 10.1002/pro.4285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/13/2022]
Abstract
GFP‐like chromoproteins (CPs) with non‐fluorescence ability have been used as bioimaging probes. Existing CPs have voids in the optical absorption window which limits their extensibility. The development of new CP color is therefore ongoing. Here, we cloned CPs from the jellyfish, Olindias formosa, and developed a completely non‐fluorescent monomeric red CP, R‐Velour, with an absorption peak at 528 nm. To analyze the photophysical properties from a structural aspect, we determined the crystal structure of R‐Velour at a 2.1 Å resolution. R‐Velour has a trans‐chromophore similar to the green fluorescence protein, Gamillus, derived from the same jellyfish. However, in contrast to the two coplanar chromophoric rings in Gamillus, R‐Velour has a large torsion inducing non‐fluorescence property. Through site‐directed mutagenesis, we surveyed residues surrounding the chromophore and found a key residue, Ser155, which contributes to the generation of four‐color variants with the bathochromic and hypsochromic shift of the absorption peak, ranging from 506 to 554 nm. The recently proposed spectrum shift theory, based on the Marcus–Hush model, supports the spectrum shift of these mutants. These findings may support further development of R‐Velour variants with useful absorption characteristics for bioimaging, including fluorescence lifetime imaging and photoacoustic imaging.
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Affiliation(s)
- Le Zhai
- Graduate School of Frontier Bioscience Osaka University Suita Japan
- SANKEN (The Institute of Scientific and Industrial Research) Osaka University Ibaraki Japan
| | - Ryosuke Nakashima
- SANKEN (The Institute of Scientific and Industrial Research) Osaka University Ibaraki Japan
| | - Hajime Shinoda
- SANKEN (The Institute of Scientific and Industrial Research) Osaka University Ibaraki Japan
| | - Yoshimasa Ike
- SANKEN (The Institute of Scientific and Industrial Research) Osaka University Ibaraki Japan
- Department of Biotechnology Graduate School of Engineering, Osaka University Suita Japan
| | - Tomoki Matsuda
- SANKEN (The Institute of Scientific and Industrial Research) Osaka University Ibaraki Japan
- Department of Biotechnology Graduate School of Engineering, Osaka University Suita Japan
| | - Takeharu Nagai
- Graduate School of Frontier Bioscience Osaka University Suita Japan
- SANKEN (The Institute of Scientific and Industrial Research) Osaka University Ibaraki Japan
- Department of Biotechnology Graduate School of Engineering, Osaka University Suita Japan
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8
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Generation of a human SOX10 knock-in reporter iPSC line for visualization of neural crest cell differentiation. Stem Cell Res 2022; 60:102696. [DOI: 10.1016/j.scr.2022.102696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/27/2021] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
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9
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Kamiya D, Yamashita T, Akaboshi T, Yamaguchi Y, Toyooka Y, Ikeya M. Generation of human GAPDH knock-in reporter iPSC lines for stable expression of tdTomato in pluripotent and differentiated culture conditions. Stem Cell Res 2022; 60:102704. [PMID: 35176664 DOI: 10.1016/j.scr.2022.102704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/03/2022] [Indexed: 11/29/2022] Open
Abstract
Human induced pluripotent stem cells (iPSCs) can differentiate into multiple cell types and are utilized for research on human development and regenerative medicine. Here, we report the establishment of human GAPDH knock-in reporter iPSC lines (GAPDH-tdT1 and 2), via CRISPR/Cas9-mediated homologous recombination, that stably express tdTomato as a constitutive cell label in both iPSCs and their differentiated derivatives. These cell lines will provide useful tools to trace cell locations and fates in 2D cultures and 3D organoids and will facilitate in vivo experiments.
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Affiliation(s)
- Daisuke Kamiya
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan.
| | - Teruyoshi Yamashita
- T-CiRA Discovery, Takeda Pharmaceutical Co. Ltd, Fujisawa, Kanagawa, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | - Teppei Akaboshi
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | | | - Yayoi Toyooka
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | - Makoto Ikeya
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
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10
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Roldán‐Salgado A, Muslinkina L, Pletnev S, Pletneva N, Pletnev V, Gaytán P. A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins. Protein Sci 2022; 31:688-700. [PMID: 34936154 PMCID: PMC8862416 DOI: 10.1002/pro.4265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
Abstract
We describe an engineered violet fluorescent protein from the lancelet Branchiostoma floridae (bfVFP). This is the first example of a GFP-like fluorescent protein with a stable fluorescent chromophore lacking an imidazolinone ring; instead, it consists of oxidized tyrosine 68 flanked by glycine 67 and alanine 69. bfVFP contains the simplest chromophore reported in fluorescent proteins and was generated from the yellow protein lanFP10A2 by two synergetic mutations, S148H and C166I. The chromophore structure was confirmed crystallographically and by high-resolution mass spectrometry. The photophysical characteristics of bfVFP (323/430 nm, quantum yield 0.33, and Ec 14,300 M-1 cm-1 ) make it potentially useful for multicolor experiments to expand the excitation range of available FP biomarkers and Förster resonance energy transfer with blue and cyan fluorescent protein acceptors.
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Affiliation(s)
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies BranchNational Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Nadya Pletneva
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Vladimir Pletnev
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Paul Gaytán
- Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
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11
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Konen T, Stumpf D, Grotjohann T, Jansen I, Bossi M, Weber M, Jensen N, Hell SW, Jakobs S. The Positive Switching Fluorescent Protein Padron2 Enables Live-Cell Reversible Saturable Optical Linear Fluorescence Transitions (RESOLFT) Nanoscopy without Sequential Illumination Steps. ACS NANO 2021; 15:9509-9521. [PMID: 34019380 PMCID: PMC8291764 DOI: 10.1021/acsnano.0c08207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Reversibly switchable fluorescent proteins (RSFPs) can be repeatedly transferred between a fluorescent on- and a nonfluorescent off-state by illumination with light of different wavelengths. Negative switching RSFPs are switched from the on- to the off-state with the same wavelength that also excites fluorescence. Positive switching RSFPs have a reversed light response, where the fluorescence excitation wavelength induces the transition from the off- to the on-state. Reversible saturable optical linear (fluorescence) transitions (RESOLFT) nanoscopy utilizes these switching states to achieve diffraction-unlimited resolution but so far has primarily relied on negative switching RSFPs by using time sequential switching schemes. On the basis of the green fluorescent RSFP Padron, we engineered the positive switching RSFP Padron2. Compared to its predecessor, it can undergo 50-fold more switching cycles while displaying a contrast ratio between the on- and the off-states of more than 100:1. Because of its robust switching behavior, Padron2 supports a RESOLFT imaging scheme that entirely refrains from sequential switching as it only requires beam scanning of two spatially overlaid light distributions. Using Padron2, we demonstrate live-cell RESOLFT nanoscopy without sequential illumination steps.
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Affiliation(s)
- Timo Konen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Daniel Stumpf
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Tim Grotjohann
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Isabelle Jansen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Mariano Bossi
- Department
of Optical Nanoscopy, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Michael Weber
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Nickels Jensen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
- Department
of Optical Nanoscopy, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefan Jakobs
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
- Clinic
of Neurology, University of Göttingen, 37075 Göttingen, Germany
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12
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Gruber DF, Sparks JS. First Report of Biofluorescence in Arctic Snailfishes and Rare Occurrence of Multiple Fluorescent Colors in a Single Species. AMERICAN MUSEUM NOVITATES 2021. [DOI: 10.1206/3967.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- David F. Gruber
- Department of Natural Sciences, Baruch College and the Graduate Center, City University of New York
| | - John S. Sparks
- Sackler Institute for Comparative Genomics, American Museum of Natural History
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13
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Gorbachev DA, Petrusevich EF, Kabylda AM, Maksimov EG, Lukyanov KA, Bogdanov AM, Baranov MS, Bochenkova AV, Mishin AS. A General Mechanism of Green-to-Red Photoconversions of GFP. Front Mol Biosci 2020; 7:176. [PMID: 32850965 PMCID: PMC7405548 DOI: 10.3389/fmolb.2020.00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Here we dissect the phenomena of oxidative and reductive green-to-red photoconversion of the Green Fluorescent Protein. We characterize distinct orange- and red-emitting forms (λabs/λem = 490/565 nm; λabs/λem = 535/600 nm) arising during the Enhanced Green Fluorescent Protein (EGFP) photoconversion under low-oxygen conditions in the presence of reductants. These forms spectroscopically differ from that observed previously in oxidative redding (λabs/λem = 575/607 nm). We also report on a new green-emitting state (λabs/λem = 405/525 nm), which is formed upon photoconversion under the low-oxygen conditions. Based on the spectral properties of these forms, their light-independent time evolution, and the high-level computational studies, we provide a structural basis for various photoproducts. Under the low-oxygen conditions, the neutral quinoid-like structure formed via a two-electron oxidation process is found to be a key intermediate and a most likely candidate for the novel green-emitting state of the chromophore. The observed large Stokes shift is traced to the formation of the zwitterionic form of the chromophore in the excited state. Subsequently, this form undergoes two types of cyclization reactions, resulting in the formation of either the orange-emitting state (λabs/λem = 490/565 nm) or the red-emitting form (λabs/λem = 535/600 nm). The T65G mutant lacks one of the proposed cyclization pathways and, indeed, the photoconverted T65G EGFP exhibits a single orange-emitting state. In oxidative redding, the red-emitting state resembles the structure of the chromophore from asFP595 (λabs/λem = 572/595 nm), which is directly formed upon two-electron oxidation and deprotonation bypassing the formation of the quinoid-like structure. Our results disclose a general “oxidative” mechanism of various green-to-red photoconversions of EGFP, providing a link between oxidative redding and the photoconversion under low-oxygen conditions.
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Affiliation(s)
- Dmitry A Gorbachev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Adil M Kabylda
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Eugene G Maksimov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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14
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Chaturvedi VK, Singh A, Singh VK, Singh MP. Cancer Nanotechnology: A New Revolution for Cancer Diagnosis and Therapy. Curr Drug Metab 2020; 20:416-429. [PMID: 30227814 DOI: 10.2174/1389200219666180918111528] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/01/2018] [Accepted: 08/20/2018] [Indexed: 01/04/2023]
Abstract
BACKGROUND Nanotechnology is gaining significant attention worldwide for cancer treatment. Nanobiotechnology encourages the combination of diagnostics with therapeutics, which is a vital component of a customized way to deal with the malignancy. Nanoparticles are being used as Nanomedicine which participates in diagnosis and treatment of various diseases including cancer. The unique characteristic of Nanomedicine i.e. their high surface to volume ratio enables them to tie, absorb, and convey small biomolecule like DNA, RNA, drugs, proteins, and other molecules to targeted site and thus enhances the efficacy of therapeutic agents. OBJECTIVE The objective of the present article is to provide an insight of several aspect of nanotechnology in cancer therapeutics such as various nanomaterials as drug vehicle, drug release strategies and role of nanotechnology in cancer therapy. METHODS We performed an extensive search on bibliographic database for research article on nanotechnology and cancer therapeutics and further compiled the necessary information from various articles into the present article. RESULTS Cancer nanotechnology confers a unique technology against cancer through early diagnosis, prevention, personalized therapy by utilizing nanoparticles and quantum dots.Nano-biotechnology plays an important role in the discovery of cancer biomarkers. Quantum dots, gold nanoparticles, magnetic nanoparticles, carbon nanotubes, gold nanowires etc. have been developed as a carrier of biomolecules that can detect cancer biomarkers. Nanoparticle assisted cancer detection and monitoring involves biomolecules like proteins, antibody fragments, DNA fragments, and RNA fragments as the base of cancer biomarkers. CONCLUSION This review highlights various approaches of cancer nanotechnology in the advancement of cancer therapy.
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Affiliation(s)
- Vivek K Chaturvedi
- Centre of Biotechnology, University of Allahabad, Allahabad-211002, India
| | - Anshuman Singh
- Centre of Biotechnology, University of Allahabad, Allahabad-211002, India
| | - Vinay K Singh
- CMP Degree College, University of Allahabad, Allahabad-211002, India
| | - Mohan P Singh
- Centre of Biotechnology, University of Allahabad, Allahabad-211002, India
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15
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Novel Phototransformable Fluorescent Protein SAASoti with Unique Photochemical Properties. Int J Mol Sci 2019; 20:ijms20143399. [PMID: 31373280 PMCID: PMC6678895 DOI: 10.3390/ijms20143399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022] Open
Abstract
SAASoti is a unique fluorescent protein (FP) that combines properties of green-to-red photoconversion and reversible photoswitching (in its green state), without any amino acid substitutions in the wild type gene. In the present work, we investigated its ability to photoswitch between fluorescent red (‘on’) and dark (‘off’) states. Surprisingly, generated by 400 nm exposure, the red form of SAASoti (R1) does not exhibit any reversible photoswitching behavior under 550 nm illumination, while a combination of prior 470 nm and subsequent 400 nm irradiation led to the appearance of another—R2—form that can be partially photoswitched (550 nm) to the dark state, with a very fast recovery time. The phenomenon might be explained by chemical modification in the chromophore microenvironment during prior 470 nm exposure, and the resulting R2 SAASoti differs chemically from the R1 form. The suggestion is supported by the mass spectrometry analysis of the tryptic peptides before and after 470 nm light exposure, that revealed Met164 oxidation, as proceeds in another dual phototransformable FP, IrisFP.
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16
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Jradi FM, Lavis LD. Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy. ACS Chem Biol 2019; 14:1077-1090. [PMID: 30997987 DOI: 10.1021/acschembio.9b00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing "super-resolution" fluorescence microscopy below the diffraction limit of light. The past decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.
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Affiliation(s)
- Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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17
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Chang HY, Ko TP, Chang YC, Huang KF, Lin CY, Chou HY, Chiang CY, Tsai HJ. Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni. Int J Biol Macromol 2019; 130:675-684. [PMID: 30836182 DOI: 10.1016/j.ijbiomac.2019.02.138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 11/15/2022]
Abstract
Chromoproteins are a good source of engineered biological tools. We previously reported the development of a blue fluorescent protein, termed shBFP, which was derived from a purple chromoprotein shCP found in the sea anemone Stichodacyla haddoni. shBFP contains a Leu63-Leu64-Gly65 tri-peptide chromophore, and shows maximum excitation and emission wavelengths at 401 nm and 458 nm, along with a high quantum yield. How this chromophore endows shBFP with the unique fluorescence property in the absence of a hydroxyphenyl ring remained unclear. Here, we present the crystal structures of shCP and shBFP at 1.9- and 2.05-Å resolution, respectively. Both proteins crystallized as similar tetramers, but they are more likely to function as dimers in solution. The chromophore in shCP shows a trans-conformation and its non-planarity is similar to most other homologues. The shBFP chromophore also contains an imidazolidone moiety in its structure, but there are a smaller number of conjugated double bonds compared to shCP. Consequently, the chromophore may prefer absorbing shorter wavelength lights in the UV region, followed by the emission of blue fluorescence. These observations provide new insights into the molecular basis that correlates chromophore conformation with light absorption and fluorescence emission for the development of improved biomarkers.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan; The Asia-Pacific Ocean Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan; Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ching Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Cheng-Yung Lin
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
| | - Hong-Yun Chou
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Cheng-Yi Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan.
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18
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Mishra K, Fuenzalida-Werner JP, Ntziachristos V, Stiel AC. Photocontrollable Proteins for Optoacoustic Imaging. Anal Chem 2019; 91:5470-5477. [PMID: 30933491 DOI: 10.1021/acs.analchem.9b01048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Photocontrollable proteins revolutionized life-science imaging due to their contribution to subdiffraction-resolution optical microscopy. They might have yet another lasting impact on photo- or optoacoustic imaging (OA). OA combines optical contrast with ultrasound detection enabling high-resolution real-time in vivo imaging well-beyond the typical penetration depth of optical methods. While OA already showed numerous applications relying on endogenous contrast from blood hemoglobin or lipids, its application in the life-science was limited by a lack of labels overcoming the strong signal from the aforementioned endogenous absorbers. Here, a number of recent studies showed that photocontrollable proteins provide the means to overcome this barrier eventually enabling OA to image small cell numbers in a complete organism in vivo. In this Feature article, we introduce the key photocontrollable proteins, explain the basic concepts, and highlight achievements that have been already made.
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Affiliation(s)
- Kanuj Mishra
- Institute of Biological and Medical Imaging (IBMI) , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | | | - Vasilis Ntziachristos
- Institute of Biological and Medical Imaging (IBMI) , Helmholtz Zentrum München , 85764 Neuherberg , Germany.,Chair of Biological Imaging and Center for Translational Cancer Research (TranslaTUM) , Technische Universität München , 81675 Munich , Germany
| | - Andre C Stiel
- Institute of Biological and Medical Imaging (IBMI) , Helmholtz Zentrum München , 85764 Neuherberg , Germany
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19
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Sahl SJ, Schönle A, Hell SW. Fluorescence Microscopy with Nanometer Resolution. SPRINGER HANDBOOK OF MICROSCOPY 2019. [DOI: 10.1007/978-3-030-00069-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Ingerman EA, London RA, Heintzmann R, Gustafsson MGL. Signal, noise and resolution in linear and nonlinear structured-illumination microscopy. J Microsc 2019; 273:3-25. [PMID: 30153327 DOI: 10.1111/jmi.12753] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 02/01/2023]
Abstract
Structured-illumination microscopy allows widefield fluorescence imaging with resolution beyond the classical diffraction limit. Its linear form extends resolution by a factor of two, and its nonlinear form by an in-principle infinite factor, the effective resolution in practice being determined by noise. In this paper, we analyse the noise properties and achievable resolution of linear and nonlinear 1D and 2D patterned SIM from a frequency-space perspective. We develop an analytical theory for a general case of linear or nonlinear fluorescent imaging, and verify the analytical calculations with numerical simulation for a special case where nonlinearity is produced by photoswitching of fluorescent labels. We compare the performance of two alternative implementations, using either two-dimensional (2D) illumination patterns or sequentially rotated one-dimensional (ID) patterns. We show that 1D patterns are advantageous in the linear case, and that in the nonlinear case 2D patterns provide a slight signal-to-noise advantage under idealised conditions, but perform worse than 1D patterns in the presence of nonswitchable fluorescent background. LAY DESCRIPTION: Structured-illumination microscopy (SIM) is a high-resolution light microscopy technique that allows imaging of fluorescence at a resolution about twice the classical diffraction limit. There are various ways that the illumination can be structured, but it is not obvious how the choice of illumination pattern affects the final image quality, especially in view of the noise. We present a detailed performance analysis considering two illumination techniques: sequential illumination with line-gratings that are shifted and rotated during image acquisition and two-dimensional (2D) illumination structures requiring only shift operations. Our analysis is based on analytical theory, supported by simulations of images considering noise. We also extend our analysis to a nonlinear variant of SIM, with which enhanced resolution can be achieved, limited only by noise. This includes nonlinear SIM based on the light-induced switching of the fluorescent molecules between a bright and a dark state. We find sequential illumination with line-gratings to be advantageous in ordinary (linear) SIM, whereas 2D patterns provides a slight signal-to-noise advantage under idealised conditions in nonlinear SIM if there is no nonswitching background.
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Affiliation(s)
- E A Ingerman
- Center for Biophotonics Science and Technology, University of California Davis, Davis, California, U.S.A
| | - R A London
- Lawrence Livermore National Laboratory, Livermore, California, U.S.A
| | - R Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, Jena, Germany
| | - M G L Gustafsson
- Department of Physiology and Program in Bioengineering, University of California San Francisco, San Francisco, California, U.S.A
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, U.S.A
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21
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Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems. Nat Commun 2018; 9:3281. [PMID: 30115928 PMCID: PMC6095837 DOI: 10.1038/s41467-018-05799-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/27/2018] [Indexed: 11/15/2022] Open
Abstract
The theoretically unlimited spatial resolution of fluorescence nanoscopy often comes at the expense of time, contrast and increased dose of energy for recording. Here, we developed MoNaLISA, for Molecular Nanoscale Live Imaging with Sectioning Ability, a nanoscope capable of imaging structures at a scale of 45–65 nm within the entire cell volume at low light intensities (W-kW cm−2). Our approach, based on reversibly switchable fluorescent proteins, features three distinctly modulated illumination patterns crafted and combined to gain fluorescence ON–OFF switching cycles and image contrast. By maximizing the detected photon flux, MoNaLISA enables prolonged (40–50 frames) and large (50 × 50 µm2) recordings at 0.3–1.3 Hz with enhanced optical sectioning ability. We demonstrate the general use of our approach by 4D imaging of organelles and fine structures in epithelial human cells, colonies of mouse embryonic stem cells, brain cells, and organotypic tissues. Super-resolution microscopy often suffers from low contrast and slow recording times. Here the authors present an optical implementation which makes the fluorescent proteins’ ON–OFF switching cycles more efficient, enhancing contrast and spatio-temporal resolution in 3D cell and tissue imaging.
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22
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Liljeruhm J, Funk SK, Tietscher S, Edlund AD, Jamal S, Wistrand-Yuen P, Dyrhage K, Gynnå A, Ivermark K, Lövgren J, Törnblom V, Virtanen A, Lundin ER, Wistrand-Yuen E, Forster AC. Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology. J Biol Eng 2018; 12:8. [PMID: 29760772 PMCID: PMC5946454 DOI: 10.1186/s13036-018-0100-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/23/2018] [Indexed: 01/14/2023] Open
Abstract
Background Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Förster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field. Most near-term applications of CPs require expression in a different domain of life: bacteria. However, it is unclear which of the eukaryotic CP genes might be suitable and how best to assay them. Results Here, taking advantage of codon optimization programs in 12 cases, we engineered 14 CP sequences (meffRed, eforRed, asPink, spisPink, scOrange, fwYellow, amilGFP, amajLime, cjBlue, meffBlue, aeBlue, amilCP, tsPurple and gfasPurple) into a palette of Escherichia coli BioBrick plasmids. BioBricks comply with synthetic biology’s most widely used, simplified, cloning standard. Differences in color intensities, maturation times and fitness costs of expression were compared under the same conditions, and visible readout of gene expression was quantitated. A surprisingly large variation in cellular fitness costs was found, resulting in loss of color in some overnight liquid cultures of certain high-copy-plasmid-borne CPs, and cautioning the use of multiple CPs as markers in competition assays. We solved these two problems by integrating pairs of these genes into the chromosome and by engineering versions of the same CP with very different colors. Conclusion Availability of 14 engineered CP genes compared in E. coli, together with chromosomal mutants suitable for competition assays, should simplify and expand CP study and applications. There was no single plasmid-borne CP that combined all of the most desirable features of intense color, fast maturation and low fitness cost, so this study should help direct future engineering efforts. Electronic supplementary material The online version of this article (10.1186/s13036-018-0100-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Josefine Liljeruhm
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Saskia K Funk
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sandra Tietscher
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anders D Edlund
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | - Sabri Jamal
- 2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | | | - Karl Dyrhage
- 2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | - Arvid Gynnå
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,2iGEM Uppsala, Uppsala University, Uppsala, Sweden
| | | | - Jessica Lövgren
- 3Biology Education Centre at Uppsala University, Uppsala, Sweden
| | - Viktor Törnblom
- 3Biology Education Centre at Uppsala University, Uppsala, Sweden
| | - Anders Virtanen
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Erik R Lundin
- 2iGEM Uppsala, Uppsala University, Uppsala, Sweden.,4Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Wistrand-Yuen
- 4Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Anthony C Forster
- 1Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,5Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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23
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Fanjiang MW, Li MJ, Sung R, Sung K. Synthesis and properties of the para-trimethylammonium analogues of green fluorescence protein (GFP) chromophore: The mimic of protonated GFP chromophore. Bioorg Chem 2018; 77:300-310. [DOI: 10.1016/j.bioorg.2018.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 01/27/2023]
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24
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Mallien C, Porro B, Zamoum T, Olivier C, Wiedenmann J, Furla P, Forcioli D. Conspicuous morphological differentiation without speciation in Anemonia viridis (Cnidaria, Actiniaria). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1383948] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Cédric Mallien
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Barbara Porro
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Thamilla Zamoum
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Caroline Olivier
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Jörg Wiedenmann
- Coral Reef Laboratory, Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Paola Furla
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Didier Forcioli
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
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25
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Suff N, Waddington SN. The power of bioluminescence imaging in understanding host-pathogen interactions. Methods 2017; 127:69-78. [PMID: 28694065 DOI: 10.1016/j.ymeth.2017.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/12/2017] [Accepted: 07/03/2017] [Indexed: 01/06/2023] Open
Abstract
Infectious diseases are one of the leading causes of death worldwide. Modelling and understanding human infection is imperative to developing treatments to reduce the global burden of infectious disease. Bioluminescence imaging is a highly sensitive, non-invasive technique based on the detection of light, produced by luciferase-catalysed reactions. In the study of infectious disease, bioluminescence imaging is a well-established technique; it can be used to detect, localize and quantify specific immune cells, pathogens or immunological processes. This enables longitudinal studies in which the spectrum of the disease process and its response to therapies can be monitored. Light producing transgenic rodents are emerging as key tools in the study of host response to infection. Here, we review the strategies for identifying biological processes in vivo, including the technology of bioluminescence imaging and illustrate how this technique is shedding light on the host-pathogen relationship.
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Affiliation(s)
- Natalie Suff
- Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, United Kingdom.
| | - Simon N Waddington
- Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, United Kingdom
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26
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Andrie RM, Martinez JP, Ciuffetti LM. Development ofToxAandToxBpromoter-driven fluorescent protein expression vectors for use in filamentous ascomycetes. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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27
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Chiang CY, Lin CY, Chen YT, Tsai HJ. Blue fluorescent protein derived from the mutated purple chromoprotein isolated from the sea anemone Stichodactyla haddoni. Protein Eng Des Sel 2016; 29:523-530. [PMID: 27578888 DOI: 10.1093/protein/gzw041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 11/14/2022] Open
Abstract
Chromoproteins, especially far-red fluorescent proteins with long stokes shift, are good sources for engineering biological research tools. However, chromoproteins have not been used for developing fluorescent proteins with short emission wavelength. Therefore, we herein report the development of a blue fluorescent protein, termed shBFP, which is derived from a purple chromoprotein isolated from the sea anemone Stichodacyla haddoni (shCP) after shCP was simultaneously mutated on E63L and Y64L. The shBFP chromophore is composed of Leu-Leu-Gly, which introduced a maximum excitation and emission wavelength at 401 nm and 458 nm, respectively, and a quantum yield of 0.79. Interestingly, the N158S and L173I double mutations of shBFP conducted in the chromophore environment further shifted the maximum excitation to 375 nm, and elevated the quantum yield to 0.84. Thus, shBFP, which is based on the Leu-Leu-Gly chromophore composition, results in higher quantum yields and short wavelength emission. Additionally, we found that the cDNA of shBFP is stably expressed in zebrafish embryos with fidelity, indicating the application of shBFP as a biomarker or selective marker.
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Affiliation(s)
- Cheng-Yi Chiang
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei106, Taiwan
| | - Cheng-Yung Lin
- Institute of Biomedical Sciences, MacKay Medical College, No. 46, Section 3, Zhongzhen Road, Sanzhi Dist., New Taipei City252, Taiwan
| | - Yen-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei106, Taiwan
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, MacKay Medical College, No. 46, Section 3, Zhongzhen Road, Sanzhi Dist., New Taipei City252, Taiwan
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28
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail. J Mol Biol 2016; 428:1776-89. [DOI: 10.1016/j.jmb.2016.02.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/27/2016] [Accepted: 02/29/2016] [Indexed: 12/11/2022]
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Pandelieva AT, Baran MJ, Calderini GF, McCann JL, Tremblay V, Sarvan S, Davey JA, Couture JF, Chica RA. Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif. ACS Chem Biol 2016; 11:508-17. [PMID: 26697759 DOI: 10.1021/acschembio.5b00774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Red fluorescent proteins (RFPs) are used extensively in chemical biology research as fluorophores for live cell imaging, as partners in FRET pairs, and as signal transducers in biosensors. For all of these applications, brighter RFP variants are desired. Here, we used rational design to increase the quantum yield of monomeric RFPs in order to improve their brightness. We postulated that we could increase quantum yield by restricting the conformational degrees of freedom of the RFP chromophore. To test our hypothesis, we introduced aromatic residues above the chromophore of mRojoA, a dim RFP containing a π-stacked Tyr residue directly beneath the chromophore, in order to reduce chromophore conformational flexibility via improved packing and steric complementarity. The best mutant identified displayed an absolute quantum yield increase of 0.07, representing an over 3-fold improvement relative to mRojoA. Remarkably, this variant was isolated following the screening of only 48 mutants, a library size that is several orders of magnitude smaller than those previously used to achieve equivalent gains in quantum yield in other RFPs. The crystal structure of the highest quantum yield mutant showed that the chromophore is sandwiched between two Tyr residues in a triple-decker motif of aromatic rings. Presence of this motif increases chromophore rigidity, as evidenced by the significantly reduced temperature factors compared to dim RFPs. Overall, the approach presented here paves the way for the rapid development of fluorescent proteins with higher quantum yield and overall brightness.
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Affiliation(s)
- Antonia T Pandelieva
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Miranda J Baran
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Guido F Calderini
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jenna L McCann
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - James A Davey
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa , 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa , 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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32
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Lin H, Yuan JM. Stochastic dynamic study of optical transition properties of single GFP-like molecules. J Biol Phys 2016; 42:271-97. [PMID: 26841730 DOI: 10.1007/s10867-015-9407-y] [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: 08/28/2015] [Accepted: 12/11/2015] [Indexed: 10/22/2022] Open
Abstract
Due to high fluctuations and quantum uncertainty, the processes of single-molecules should be treated by stochastic methods. To study fluorescence time series and their statistical properties, we have applied two stochastic methods, one of which is an analytic method to study the off-time distributions of certain fluorescence transitions and the other is Gillespie's method of stochastic simulations. These methods have been applied to study the optical transition properties of two single-molecule systems, GFPmut2 and a Dronpa-like molecule, to yield results in approximate agreement with experimental observations on these systems. Rigorous oscillatory time series of GFPmut2 before it unfolds in the presence of denaturants have not been obtained based on the stochastic method used, but, on the other hand, the stochastic treatment puts constraints on the conditions under which such oscillatory behavior is possible. Furthermore, a sensitivity analysis is carried out on GFPmut2 to assess the effects of transition rates on the observables, such as fluorescence intensities.
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Affiliation(s)
- Hanbing Lin
- Department of Physics, Drexel University, Philadelphia, PA, 19104, USA
| | - Jian-Min Yuan
- Department of Physics, Drexel University, Philadelphia, PA, 19104, USA.
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Verdes A, Cho W, Hossain M, Brennan PLR, Hanley D, Grim T, Hauber ME, Holford M. Nature's Palette: Characterization of Shared Pigments in Colorful Avian and Mollusk Shells. PLoS One 2015; 10:e0143545. [PMID: 26650398 PMCID: PMC4674117 DOI: 10.1371/journal.pone.0143545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/05/2015] [Indexed: 11/21/2022] Open
Abstract
Pigment-based coloration is a common trait found in a variety of organisms across the tree of life. For example, calcareous avian eggs are natural structures that vary greatly in color, yet just a handful of tetrapyrrole pigment compounds are responsible for generating this myriad of colors. To fully understand the diversity and constraints shaping nature's palette, it is imperative to characterize the similarities and differences in the types of compounds involved in color production across diverse lineages. Pigment composition was investigated in eggshells of eleven paleognath bird taxa, covering several extinct and extant lineages, and shells of four extant species of mollusks. Birds and mollusks are two distantly related, calcareous shell-building groups, thus characterization of pigments in their calcareous structures would provide insights to whether similar compounds are found in different phyla (Chordata and Mollusca). An ethylenediaminetetraacetic acid (EDTA) extraction protocol was used to analyze the presence and concentration of biliverdin and protoporphyrin, two known and ubiquitous tetrapyrrole avian eggshell pigments, in all avian and molluscan samples. Biliverdin was solely detected in birds, including the colorful eggshells of four tinamou species. In contrast, protoporphyrin was detected in both the eggshells of several avian species and in the shells of all mollusks. These findings support previous hypotheses about the ubiquitous deposition of tetrapyrroles in the eggshells of various bird lineages and provide evidence for its presence also across distantly related animal taxa.
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Affiliation(s)
- Aida Verdes
- The Graduate Center, City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Wooyoung Cho
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
| | - Marouf Hossain
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
| | - Patricia L. R. Brennan
- Department of Psychology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Daniel Hanley
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic
| | - Tomáš Grim
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic
| | - Mark E. Hauber
- The Graduate Center, City University of New York, New York, New York, United States of America
- Department of Psychology, Hunter College, City University of New York, New York, New York, United States of America
| | - Mandë Holford
- The Graduate Center, City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
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Gruber DF, Gaffney JP, Mehr S, DeSalle R, Sparks JS, Platisa J, Pieribone VA. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment. PLoS One 2015; 10:e0140972. [PMID: 26561348 PMCID: PMC4641735 DOI: 10.1371/journal.pone.0140972] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/02/2015] [Indexed: 11/23/2022] Open
Abstract
We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs) from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs). Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp.), two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II). We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein’s fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.
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Affiliation(s)
- David F. Gruber
- Baruch College, Department of Natural Sciences, City University of New York, New York, New York, United States of America
- The Graduate Center, Program in Biology, City University of New York, New York, New York, United States of America
- American Museum of Natural History, Sackler Institute for Comparative Genomics,Central Park W at 79th St, New York, New York, United States of America
- * E-mail:
| | - Jean P. Gaffney
- Baruch College, Department of Natural Sciences, City University of New York, New York, New York, United States of America
| | - Shaadi Mehr
- State University of New York, Biological Science Department, College at Old Westbury, Old Westbury, New York, United States of America
- American Museum of Natural History, Sackler Institute for Comparative Genomics,Central Park W at 79th St, New York, New York, United States of America
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics,Central Park W at 79th St, New York, New York, United States of America
| | - John S. Sparks
- American Museum of Natural History, Sackler Institute for Comparative Genomics,Central Park W at 79th St, New York, New York, United States of America
- American Museum of Natural History, Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut, United States of America
| | - Vincent A. Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut, United States of America
- Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
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35
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Chiang CY, Lee CC, Lo SY, Wang AHJ, Tsai HJ. Chromophore Deprotonation State Alters the Optical Properties of Blue Chromoprotein. PLoS One 2015. [PMID: 26218063 PMCID: PMC4517874 DOI: 10.1371/journal.pone.0134108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromoproteins (CPs) have unique colors and can be used in biological applications. In this work, a novel blue CP with a maximum absorption peak (λmax) at 608 nm was identified from the carpet anemone Stichodactyla gigantea (sgBP). In vivo expression of sgBP in zebrafish would change the appearance of the fishes to have a blue color, indicating the potential biomarker function. To enhance the color properties, the crystal structure of sgBP at 2.25 Å resolution was determined to allow structure-based protein engineering. Among the mutations conducted in the Gln-Tyr-Gly chromophore and chromophore environment, a S157C mutation shifted the λmax to 604 nm with an extinction coefficient (ε) of 58,029 M-1·cm-1 and darkened the blue color expression. The S157C mutation in the sgBP chromophore environment could affect the color expression by altering the deprotonation state of the phenolic group in the chromophore. Our results provide a structural basis for the blue color enhancement of the biomarker development.
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Affiliation(s)
- Cheng-Yi Chiang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei, Taiwan
| | - Shin-Yi Lo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei, Taiwan
- * E-mail: (HJT); (AHJW)
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
- * E-mail: (HJT); (AHJW)
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36
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Mironov VA, Bravaya KB, Nemukhin AV. Role of Zwitterions in Kindling Fluorescent Protein Photochemistry. J Phys Chem B 2014; 119:2467-74. [DOI: 10.1021/jp5075219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vladimir A. Mironov
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
| | - Ksenia B. Bravaya
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Alexander V. Nemukhin
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
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37
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Chiang CY, Chen YL, Tsai HJ. Different visible colors and green fluorescence were obtained from the mutated purple chromoprotein isolated from sea anemone. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:436-446. [PMID: 24488042 DOI: 10.1007/s10126-014-9563-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/06/2014] [Indexed: 06/03/2023]
Abstract
Green fluorescent protein (GFP)-like proteins have been studied with the aim of developing fluorescent proteins. Since the property of color variation is understudied, we isolated a novel GFP-like chromoprotein from the carpet anemone Stichodactyla haddoni, termed shCP. Its maximum absorption wavelength peak (λ(max)) is located at 574 nm, resulting in a purple color. The shCP protein consists of 227 amino acids (aa), sharing 96 % identity with the GFP-like chromoprotein of Heteractis crispa. We mutated aa residues to examine any alteration in color. When E63, the first aa of the chromophore, was replaced by serine (E63S), the λ(max) of the mutated protein shCP-E63S was shifted to 560 nm and exhibited a pink color. When Q39, T194, and I196, which reside in the surrounding 5 Å of the chromophore's microenvironment, were mutated, we found that (1) the λ(max) of the mutated protein shCP-Q39S was shifted to 518 nm and exhibited a red color, (2) shCP-T194I exhibited a purple-blue color, and (3) an additional mutation at I196H of the mutated protein shCP-E63L exhibited green fluorescence. In contrast, when the aa located neither at the chromophore nor within its microenvironment were mutated, the resultant proteins shCP-L122H, -E138G, -S137D, -T95I, -D129N, -T194V, -E138Q, -G75E, -I183V, and -I70V never altered their purple color, suggesting that mutations at the shCP chromophore and the surrounding 5 Å microenvironment mostly control changes in color expression or cause fluorescence to develop. Additionally, we found that the cDNAs of shCP and its mutated varieties are faithfully and stably expressed both in Escherichia coli and zebrafish embryos.
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Affiliation(s)
- Cheng-Yi Chiang
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 106, Taiwan
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38
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Tzima AK, Paplomatas EJ, Schoina C, Domazakis E, Kang S, Goodwin PH. Successful Agrobacterium mediated transformation of Thielaviopsis basicola by optimizing multiple conditions. Fungal Biol 2014; 118:675-82. [PMID: 25110130 DOI: 10.1016/j.funbio.2014.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 03/02/2014] [Accepted: 04/22/2014] [Indexed: 11/15/2022]
Abstract
Thielaviopsis basicola is a hemibiotrophic root pathogen causing black root rot in a wide range of economically important crops. Our initial attempts to transform T. basicola using standard Agrobacterium tumefaciens-mediated transformation (ATMT) protocols were unsuccessful. Successful transformation required the addition of V8 juice (to induce germination of T. basicola chlamydospores) and higher concentrations of acetosyringone in the co-cultivation medium, and of chlamydospores/endoconidia, A. tumefaciens cells during co-cultivation. With these modifications, two T. basicola strains were successfully transformed with the green (egfp) or red (AsRed) fluorescent protein genes. Chlamydospores/endoconidia transformed with the egfp gene exhibited strong green fluorescence, but their fluorescence became weaker as the germ tubes emerged. Transformants harbouring the AsRed gene displayed strong red fluorescence in both chlamydospores/endoconidia and germ tubes. Fluorescent microscopic observations of an AsRed-labelled strain colonizing roots of transgenic Nicotiana benthamiana plants, which express the actin filaments labelled with EGFP, at 24 hours post inoculation showed varying levels of fungal germination and penetration. At this stage, the infection appeared to be biotrophic with the EGFP-labelled host actin filaments not being visibly degraded, even in host root cells in close contact with the hyphae. This is the first report of ATMT of T. basicola, and the use of an AsRed-labelled strain to directly observe the root infection process.
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Affiliation(s)
- Aliki K Tzima
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece.
| | - Epaminondas J Paplomatas
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Charikleia Schoina
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Emmanouil Domazakis
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Seogchan Kang
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Paul H Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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Hedde PN, Nienhaus GU. Super-resolution localization microscopy with photoactivatable fluorescent marker proteins. PROTOPLASMA 2014; 251:349-62. [PMID: 24162869 DOI: 10.1007/s00709-013-0566-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 05/02/2023]
Abstract
Fluorescent proteins (FPs) have become popular imaging tools because of their high specificity, minimal invasive labeling and allowing visualization of proteins and structures inside living organisms. FPs are genetically encoded and expressed in living cells, therefore, labeling involves minimal effort in comparison to approaches involving synthetic dyes. Photoactivatable FPs (paFPs) comprise a subclass of FPs that can change their absorption/emission properties such as brightness and color upon irradiation. This methodology has found a broad range of applications in the life sciences, especially in localization-based super-resolution microscopy of cells, tissues and even entire organisms. In this review, we discuss recent developments and applications of paFPs in super-resolution localization imaging.
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Affiliation(s)
- Per Niklas Hedde
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
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40
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Adam V. Phototransformable fluorescent proteins: which one for which application? Histochem Cell Biol 2014; 142:19-41. [PMID: 24522394 DOI: 10.1007/s00418-014-1190-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 01/10/2023]
Abstract
In these last two decades , fluorescent proteins (FPs) have become highly valued imaging tools for cell biology, owing to their compatibility with living samples, their low levels of invasiveness and the possibility to specifically fuse them to a variety of proteins of interest. Remarkably, the recent development of phototransformable fluorescent proteins (PTFPs) has made it possible to conceive optical imaging experiments that were unimaginable only a few years ago. For example, it is nowadays possible to monitor intra- or intercellular trafficking, to optically individualize single cells in tissues or to observe single molecules in live cells. The tagging specificity brought by these genetically encoded highlighters leads to constant progress in the engineering of increasingly powerful, versatile and non-cytotoxic FPs. This review is focused on the recent developments of PTFPs and highlights their contribution to studies within cells, tissues and even living organisms. The aspects of single-molecule localization microscopy, intracellular tracking of photoactivated molecules, applications of PTFPs in biotechnology/optobiology and complementarities between PTFPs and other microscopy techniques are particularly discussed.
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Affiliation(s)
- Virgile Adam
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, F-38000, Grenoble, France,
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41
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Duan C, Adam V, Byrdin M, Bourgeois D. Structural basis of photoswitching in fluorescent proteins. Methods Mol Biol 2014; 1148:177-202. [PMID: 24718802 DOI: 10.1007/978-1-4939-0470-9_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fluorescent proteins have revolutionized life sciences because they allow noninvasive and highly specific labeling of biological samples. The subset of "phototransformable" fluorescent proteins recently attracted a widespread interest, as their fluorescence state can be modified upon excitation at defined wavelengths. The fluorescence emission of Reversibly Switchable Fluorescent Proteins (RSFPs), in particular, can be repeatedly switched on and off. RSFPs enable many new exciting modalities in fluorescence microscopy and biotechnology, including protein tracking, photochromic Förster Resonance Energy Transfer, super-resolution microscopy, optogenetics, and ultra-high-density optical data storage. Photoswitching in RSFPs typically results from chromophore cis-trans isomerization accompanied by a protonation change, but other switching schemes based on, e.g., chromophore hydration/dehydration have also been discovered. In this chapter, we review the main structural features at the basis of photoswitching in RSFPs.
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Affiliation(s)
- Chenxi Duan
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
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42
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Nowotschin S, Hadjantonakis AK. Live imaging mouse embryonic development: seeing is believing and revealing. Methods Mol Biol 2014; 1092:405-20. [PMID: 24318833 DOI: 10.1007/978-1-60327-292-6_24] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The use of genetically encoded fluorescent proteins has revolutionized the fields of cell and developmental biology and redefined our understanding of the dynamic morphogenetic processes that work to shape the embryo. Fluorescent proteins are routinely used as vital reporters to label tissues, cells, cellular organelles, or proteins of interest and in doing so provide contrasting agents enabling the acquisition of high-resolution quantitative image data. With the advent of more accessible and sophisticated imaging technologies and abundance of fluorescent proteins with different spectral characteristics, the dynamic processes taking place in situ in living embryos can now be probed. Here, we provide an overview of some recent advances in this rapidly evolving field.
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Affiliation(s)
- Sonja Nowotschin
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA
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43
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Schüttrigkeit TA, Zachariae U, von Feilitzsch T, Wiehler J, von Hummel J, Steipe B, Michel-Beyerle ME. Picosecond time-resolved FRET in the fluorescent protein from Discosoma Red (wt-DsRed). Chemphyschem 2013; 2:325-8. [PMID: 23696507 DOI: 10.1002/1439-7641(20010518)2:5<325::aid-cphc325>3.0.co;2-p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2001] [Indexed: 11/09/2022]
Abstract
Ultrafast, intra-oligomer fluorescence resonance energy transfer (FRET) between an immature green-emitting GFP-like chromophore to the mature red-emitting chromophore is found in the novel red fluorescent protein wt-DsRed (the picture shows the steady-state absorption (solid line) and emission (dotted) spectra). Since FRET is by its very nature a short range process, it represents a highly suitable method to probe oligomerization. This work describes a method preferentially applicable to the efficient screening of protein variants with mutagenetically altered surface docking sites.
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Affiliation(s)
- T A Schüttrigkeit
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
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Mironov VA, Khrenova MG, Grigorenko BL, Savitsky AP, Nemukhin AV. Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations. J Phys Chem B 2013; 117:13507-14. [PMID: 24079704 DOI: 10.1021/jp407406k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chromoprotein asFP595 and its A143G variant called kindling fluorescent protein (KFP) are among the chronologically first species for which trans-cis chromophore isomerization has been proposed as a driving force of photoswitching. In spite of long-lasting efforts to characterize the route between protein conformations referring to the trans and cis forms of the chromophore, the molecular mechanism of this transformation is still under debate. We report the results of computational studies of the trans-cis isomerization of the anionic and neutral chromophore inside the protein matrices in the ground electronic state for both variants, asFP595 and KFP. Corresponding free energy profiles (potentials of mean force) were evaluated by using molecular dynamics simulations with the quantum mechanical-molecular mechanical (QM/MM) forces. The computed free energy barrier for the cis-trans ground state (thermal) isomerization reaction is about 2 kcal/mol higher in KFP than that in asFP595. These results provide interpretation of experimental studies on thermal relaxation from the light-induced activation of fluorescence of these proteins and correctly show that the A143G mutation in asFP595 noticeably increases the lifetime of the fluorescence species.
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Affiliation(s)
- Vladimir A Mironov
- Department of Chemistry, M.V. Lomonosov Moscow State University , Leninskie Gory, 1/3, Moscow, 119991, Russian Federation
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Highlighted Ca²⁺ imaging with a genetically encoded 'caged' indicator. Sci Rep 2013; 3:1398. [PMID: 23474844 PMCID: PMC3593221 DOI: 10.1038/srep01398] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/19/2013] [Indexed: 11/08/2022] Open
Abstract
Genetically encoded fluorescent indicators for bioimaging are powerful tools for visualizing biological phenomena in specified cell types or cellular compartments. However, available gene promoters or localization sequences are not applicable for visualizing all expression events. Furthermore, a visualization technique focusing on single cells or cellular compartments is required for characterizing specific cellular properties including individuality of cells in the cell population. To address these limitations, we developed a genetically encoded caged Ca2+ indicator for which expression timing and location could be controlled. This indicator, PA-TNXL, comprises a Ca2+-binding protein and troponin between a photoactivatable FRET donor (PA-GFP) and a FRET quencher (dim variant of YFP). Ultraviolet irradiation activates the FRET Ca2+ indicator. Using this indicator, we successfully imaged Ca2+ dynamics in a given set of HeLa cells and cultured hippocampal neurons. This technology can be applied for developing other photoactivatable indicators, thereby opening a new area of biological research.
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Zhou XX, Lin MZ. Photoswitchable fluorescent proteins: ten years of colorful chemistry and exciting applications. Curr Opin Chem Biol 2013; 17:682-90. [PMID: 23876529 DOI: 10.1016/j.cbpa.2013.05.031] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 12/12/2022]
Abstract
Reversibly photoswitchable fluorescent proteins (RSFPs) are fluorescent proteins whose fluorescence, upon excitation at a certain wavelength, can be switched on or off by light in a reversible manner. In the last 10 years, many new RSFPs have been developed and novel applications in cell imaging discovered that rely on their photoswitching properties. This review will describe research on the mechanisms of reversible photoswitching and recent applications using RSFPs. While cis-trans isomerization of the chromophore is believed to be the general mechanism for most RSFPs, structural studies reveal diversity in the details of photoswitching mechanisms, including different effects of protonation, chromophore planarity, and pocket flexibility. Applications of RSFPs include new types of live-cell superresolution imaging, tracking of protein movements and interactions, information storage, and optical control of protein activity.
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Affiliation(s)
- Xin X Zhou
- Department of Bioengineering, Stanford University, Mailcode 5164, Stanford, CA 94305, United States
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Grigorenko BL, Polyakov IV, Savitsky AP, Nemukhin AV. Unusual Emitting States of the Kindling Fluorescent Protein: Appearance of the Cationic Chromophore in the GFP Family. J Phys Chem B 2013; 117:7228-34. [DOI: 10.1021/jp402149q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bella L. Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
| | - Igor V. Polyakov
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
| | - Alexander P. Savitsky
- A.N. Bach Institute of Biochemistry of the Russian Academy of Science, Leninsky
Prospect, 33, Moscow 119071, Russian Federation
| | - Alexander V. Nemukhin
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
- N.M. Emanuel Institute of Biochemical
Physics, Russian Academy of Sciences, Kosygina
4, Moscow, 119334, Russian Federation
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Meyers M, Porter JW, Wares JP. Genetic diversity of fluorescent proteins in Caribbean agariciid corals. J Hered 2013; 104:572-7. [PMID: 23667051 DOI: 10.1093/jhered/est028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The fluorescent protein (FP) gene family is a highly diverse group of proteins whose expression govern color diversity in corals. Here, we examine the genetic diversity of FPs and the extent to which it can be used to assess phylogenetic relationships within the coral genus Agaricia. Tissue samples were collected throughout the Florida Keys from a wide range of phenotypes within the genus Agaricia (A. agaricites [n = 7], A. fragilis [n = 13], and A. lamarcki [n = 2]), as well as the confamilial species Helioseris cucullata (n = 3). Primers were developed from published cDNA sequences to amplify a region of coding and noncoding sequences of FPs. Cloning reactions were performed to capture the multiple copies of FPs and allele diversity. In the resulting 116 cloned sequences, we identified a 179-bp coding region for phylogenetic analysis. Three distinct clades were found in all 3 species of Agaricia, potentially representing 3 copies of the FP gene. Of the 3 gene copies, 2 contain distinct subclades that display reciprocal monophyly between A. agaricites and A. fragilis, whereas A. lamarcki is polyphyletic. Further resolution of the species phylogeny is necessary to fully understand how genetic diversity within this gene family is distributed among taxa and habitats.
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Affiliation(s)
- Meredith Meyers
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA.
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Dedecker P, De Schryver FC, Hofkens J. Fluorescent Proteins: Shine on, You Crazy Diamond. J Am Chem Soc 2013; 135:2387-402. [DOI: 10.1021/ja309768d] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Peter Dedecker
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Frans C. De Schryver
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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Campanini B, Pioselli B, Raboni S, Felici P, Giordano I, D'Alfonso L, Collini M, Chirico G, Bettati S. Role of histidine 148 in stability and dynamics of a highly fluorescent GFP variant. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:770-9. [PMID: 23357652 DOI: 10.1016/j.bbapap.2013.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Abstract
The armory of GFP mutants available to biochemists and molecular biologists is huge. Design and selection of mutants are usually driven by tailored spectroscopic properties, but some key aspects of stability, folding and dynamics of selected GFP variants still need to be elucidated. We have prepared, expressed and characterized three H148 mutants of the highly fluorescent variant GFPmut2. H148 is known to be involved in the H-bonding network surrounding the chromophore, and all the three mutants, H148G, H148R and H148K, show increased pKa values of the chromophore. Only H148G GFPmut2 (Mut2G) gave good expression and purification yields, indicating that position 148 is critical for efficient folding in vivo. The chemical denaturation of Mut2G was monitored by fluorescence emission, absorbance and far-UV circular dichroism spectroscopy. The mutation has little effect on the spectroscopic properties of the protein and on its stability in solution. However, the unfolding kinetics of the protein encapsulated in wet nanoporous silica gels, a system that allows to stabilize conformations that are poorly or only transiently populated in solution, indicate that the unfolding pathway of Mut2G is markedly different from the parent molecule. In particular, encapsulation allowed to identify an unfolding intermediate that retains a native-like secondary structure despite a destructured chromophore environment. Thus, H148 is a critical residue not only for the chromophoric and photodynamic properties, but also for the correct folding of GFP, and its substitution has great impact on expression yields and stability of the mature protein.
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Affiliation(s)
- Barbara Campanini
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy.
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