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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; 99:1391-1410. [PMID: 38468189 DOI: 10.1111/brv.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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2
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Fluorescent Tags in Biology: Three-Dimensional Structure. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Structure of Chromophores in GFP-Like Proteins: X-Ray Data. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201903004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Muslinkina L, Roldán-Salgado A, Gaytán P, Juárez-González VR, Rudiño E, Pletneva N, Pletnev V, Dauter Z, Pletnev S. Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue. J Mol Biol 2019; 431:1397-1408. [PMID: 30797856 PMCID: PMC6544178 DOI: 10.1016/j.jmb.2019.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/05/2019] [Accepted: 02/15/2019] [Indexed: 11/18/2022]
Abstract
GFP-like proteins from lancelets (lanFPs) is a new and least studied group that already generated several outstanding biomarkers (mNeonGreen is the brightest FP to date) and has some unique features. Here, we report the study of four homologous lanFPs with GYG and GYA chromophores. Until recently, it was accepted that the third chromophore-forming residue in GFP-like proteins should be glycine, and efforts to replace it were in vain. Now, we have the first structure of a fluorescent protein with a successfully matured chromophore that has alanine as the third chromophore-forming residue. Consideration of the protein structures revealed two alternative routes of posttranslational transformation, resulting in either chromophore maturation or hydrolysis of GYG/GYA tripeptide. Both transformations are catalyzed by the same set of catalytic residues, Arg88 and Glu35-Wat-Glu211 cluster, whereas the residues in positions 62 and 102 shift the equilibrium between chromophore maturation and hydrolysis.
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Affiliation(s)
- Liya Muslinkina
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA
| | - Abigail Roldán-Salgado
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Víctor R Juárez-González
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Enrique Rudiño
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Nadya Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Vladimir Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA.
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Schramm S, Weiß D. Fluorescent heterocycles: Recent trends and new developments. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Xia A, Han J, Jin Z, Ni L, Yang S, Jin F. Dual-Color Fluorescent Timer Enables Detection of Growth-Arrested Pathogenic Bacterium. ACS Infect Dis 2018; 4:1666-1670. [PMID: 30215505 DOI: 10.1021/acsinfecdis.8b00129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We present a method capable of detecting single slow-growing and growth-arrested cells in a bacterial culture composed of physiologically and phenotypically different cells. Unlike the use of transcriptional reporters to gauge the metabolic activities in cells, here, we fuse two different fluorescent proteins with distinctive maturation rates to construct a timer to directly determine the growth rate of single Pseudomonas aeruginosa cells. We demonstrate that the dual-color fluorescent timer can indicate the slow-growing and growth-arrested cells from bacterial cultures in the presence of various environmental stresses, including nutrient starvation or antibiotic treatments, which greatly expand the methods for detecting and isolating persister cells.
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Affiliation(s)
- Aiguo Xia
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
| | - Jundong Han
- Department of Polymer Science and Engineering, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
| | - Zhenyu Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
| | - Lei Ni
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
| | - Shuai Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
- Department of Polymer Science and Engineering, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
- CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei, Anhui 230026, P. R. China
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Kleeman B, Olsson A, Newkold T, Kofron M, DeLay M, Hildeman D, Grimes HL. A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Cytometry A 2018; 93:556-562. [PMID: 29533508 PMCID: PMC8008483 DOI: 10.1002/cyto.a.23360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/11/2022]
Abstract
The advent of facile genome engineering technologies has made the generation of knock-in gene-expression or fusion-protein reporters more tractable. Fluorescent protein labeling of specific genes combined with surface marker profiling can more specifically identify a cell population. However, the question of which fluorescent proteins to utilize to generate reporter constructs is made difficult by the number of candidate proteins and the lack of updated experimental data on newer fluorescent proteins. Compounding this problem, most fluorescent proteins are designed and tested for use in microscopy. To address this, we cloned and characterized the detection sensitivity, spectral overlap, and spillover spreading of 13 monomeric fluorescent proteins to determine utility in multicolor panels. We identified a group of five fluorescent proteins with high signal to noise ratio, minimal spectral overlap, and low spillover spreading making them compatible for multicolor experiments. Specifically, generating reporters with combinations of three of these proteins would allow efficient measurements even at low-level expression. Because the proteins are monomeric, they could function either as gene-expression or as fusion-protein reporters. Additionally, this approach can be generalized as new fluorescent proteins are developed to determine their usefulness in multicolor panels. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Benjamin Kleeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Tess Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Matt Kofron
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Monica DeLay
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - David Hildeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
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Steiert F, Petrov EP, Schultz P, Schwille P, Weidemann T. Photophysical Behavior of mNeonGreen, an Evolutionarily Distant Green Fluorescent Protein. Biophys J 2018; 114:2419-2431. [PMID: 29706225 DOI: 10.1016/j.bpj.2018.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/31/2022] Open
Abstract
Fluorescent proteins (FPs) feature complex photophysical behavior that must be considered when studying the dynamics of fusion proteins in model systems and live cells. In this work, we characterize mNeonGreen (mNG), a recently introduced FP from the bilaterian Branchiostoma lanceolatum, in comparison to the well-known hydrozoan variants enhanced green fluorescent protein (EGFP) and Aequorea coerulescens GFP by steady-state spectroscopy and fluorescence correlation spectroscopy in solutions of different pH. Blind spectral unmixing of sets of absorption spectra reveals three interconverting electronic states of mNG: a nonfluorescent protonated state, a bright state showing bell-shaped pH dependence, and a similarly bright state dominating at high pH. The gradual population of the acidic form by external protonation is reflected by increased flickering at low pH in fluorescence correlation spectroscopy measurements, albeit with much slower flicker rates and lower amplitudes as compared to Aequorea GFPs. In addition, increased flickering of mNG indicates a second deprotonation step above pH 10 leading to a slight decrease in fluorescence. Thus, mNG is distinguished from Aequorea GFPs by a two-step protonation response with opposite effects that reflects a chemically distinct chromophore environment. Despite the more complex pH dependence, mNG represents a superior FP under a broad range of conditions.
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Affiliation(s)
- Frederik Steiert
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany; Physics Department, Technical University Munich, Garching, Germany
| | - Eugene P Petrov
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Physics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Peter Schultz
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas Weidemann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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Clavel D, Gotthard G, von Stetten D, De Sanctis D, Pasquier H, Lambert GG, Shaner NC, Royant A. Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution. Acta Crystallogr D Struct Biol 2016; 72:1298-1307. [PMID: 27917830 PMCID: PMC5137226 DOI: 10.1107/s2059798316018623] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/21/2016] [Indexed: 11/10/2022] Open
Abstract
Until recently, genes coding for homologues of the autofluorescent protein GFP had only been identified in marine organisms from the phyla Cnidaria and Arthropoda. New fluorescent-protein genes have now been found in the phylum Chordata, coding for particularly bright oligomeric fluorescent proteins such as the tetrameric yellow fluorescent protein lanYFP from Branchiostoma lanceolatum. A successful monomerization attempt led to the development of the bright yellow-green fluorescent protein mNeonGreen. The structures of lanYFP and mNeonGreen have been determined and compared in order to rationalize the directed evolution process leading from a bright, tetrameric to a still bright, monomeric fluorescent protein. An unusual discolouration of crystals of mNeonGreen was observed after X-ray data collection, which was investigated using a combination of X-ray crystallography and UV-visible absorption and Raman spectroscopies, revealing the effects of specific radiation damage in the chromophore cavity. It is shown that X-rays rapidly lead to the protonation of the phenolate O atom of the chromophore and to the loss of its planarity at the methylene bridge.
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Affiliation(s)
- Damien Clavel
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
- CNRS, Laboratoire de Chimie Physique, UMR 8000 and Université Paris-Sud, F-91405 Orsay, France
| | | | | | | | - Hélène Pasquier
- CNRS, Laboratoire de Chimie Physique, UMR 8000 and Université Paris-Sud, F-91405 Orsay, France
| | - Gerard G. Lambert
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, USA
| | - Nathan C. Shaner
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, USA
| | - Antoine Royant
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
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Mishin AS, Belousov VV, Solntsev KM, Lukyanov KA. Novel uses of fluorescent proteins. Curr Opin Chem Biol 2015; 27:1-9. [PMID: 26022943 DOI: 10.1016/j.cbpa.2015.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
Abstract
The field of genetically encoded fluorescent probes is developing rapidly. New chromophore structures were characterized in proteins of green fluorescent protein (GFP) family. A number of red fluorescent sensors, for example, for pH, Ca(2+) and H2O2, were engineered for multiparameter imaging. Progress in development of microscopy hardware and software together with specially designed FPs pushed superresolution fluorescence microscopy towards fast live-cell imaging. Deeper understanding of FPs structure and photophysics led to further development of imaging techniques. In addition to commonly used GFP-like proteins, unrelated types of FPs on the base of flavin-binding domains, bilirubin-binding domains or biliverdin-binding domains were designed. Their distinct biochemical and photophysical properties opened previously unexplored niches of FP uses such as labeling under anaerobic conditions, deep tissue imaging and even patients' blood analysis.
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Affiliation(s)
- Alexander S Mishin
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Vsevolod V Belousov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332-0400, United States
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
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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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Spectral and structural comparison between bright and dim green fluorescent proteins in Amphioxus. Sci Rep 2014; 4:5469. [PMID: 24968921 PMCID: PMC4073121 DOI: 10.1038/srep05469] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 05/23/2014] [Indexed: 11/09/2022] Open
Abstract
The cephalochordate Amphioxus naturally co-expresses fluorescent proteins (FPs) with different brightness, which thus offers the rare opportunity to identify FP molecular feature/s that are associated with greater/lower intensity of fluorescence. Here, we describe the spectral and structural characteristics of green FP (bfloGFPa1) with perfect (100%) quantum efficiency yielding to unprecedentedly-high brightness, and compare them to those of co-expressed bfloGFPc1 showing extremely-dim brightness due to low (0.1%) quantum efficiency. This direct comparison of structure-function relationship indicated that in the bright bfloGFPa1, a Tyrosine (Tyr159) promotes a ring flipping of a Tryptophan (Trp157) that in turn allows a cis-trans transformation of a Proline (Pro55). Consequently, the FP chromophore is pushed up, which comes with a slight tilt and increased stability. FPs are continuously engineered for improved biochemical and/or photonic properties, and this study provides new insight to the challenge of establishing a clear mechanistic understanding between chromophore structural environment and brightness level.
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