1
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Tsuchiya K, Fujita S, Numata K. Ampholytic Peptides Consisting of an Alternating Lysine/Glutamic Acid Sequence for the Simultaneous Formation of Polyion Complex Vesicles. ACS POLYMERS AU 2024; 4:320-330. [PMID: 39156560 PMCID: PMC11328329 DOI: 10.1021/acspolymersau.4c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 08/20/2024]
Abstract
Nanoarchitectures such as micelles and vesicles that self-assemble via electrostatic interactions between their charged polymeric components have been widely used as material delivery platforms. In this work, ampholytic peptides with a sequence of alternating lysine and glutamic acid residues were designed and synthesized via chemoenzymatic polymerization. This alternating sequence was achieved by trypsin-catalyzed polymerization of a dipeptide monomer. Due to the electrostatic interaction between the anionic and cationic residues, the prepared ampholytic peptides spontaneously formed nanosized assemblies with a size of 100-200 nm in water. Modification with tetra(ethylene glycol) (TEG) at the N-terminus of these ampholytic alternating peptides resulted in the formation of stable nanosized assemblies, while peptides consisting of random sequences of lysine and glutamic acid formed large aggregates with deteriorated stability even with TEG modification. Morphological observations using a field-emission scanning electron microscope and an atomic force microscope revealed that the obtained assemblies were spherical and hollow, indicating the spontaneous formation of vesicles from the TEG-modified ampholytic alternating peptides. These vesicles were able to encapsulate a model fluorescent protein within their hollow structures without structural collapse causing loss of fluorescence, demonstrating the potential of these nanocarriers for use in material delivery systems.
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Affiliation(s)
- Kousuke Tsuchiya
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
| | - Seiya Fujita
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Keiji Numata
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
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2
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Zhao Z, Zang X, Niu K, Song W, Wang X, Mügge A, Aweimer A, Hamdani N, Zhou X, Zhao Y, Akin I, El-Battrawy I. Impacts of gene variants on drug effects-the foundation of genotype-guided pharmacologic therapy for long QT syndrome and short QT syndrome. EBioMedicine 2024; 103:105108. [PMID: 38653189 PMCID: PMC11041837 DOI: 10.1016/j.ebiom.2024.105108] [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: 08/18/2023] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 04/25/2024] Open
Abstract
The clinical significance of optimal pharmacotherapy for inherited arrhythmias such as short QT syndrome (SQTS) and long QT syndrome (LQTS) has been increasingly recognised. The advancement of gene technology has opened up new possibilities for identifying genetic variations and investigating the pathophysiological roles and mechanisms of genetic arrhythmias. Numerous variants in various genes have been proven to be causative in genetic arrhythmias. Studies have demonstrated that the effectiveness of certain drugs is specific to the patient or genotype, indicating the important role of gene-variants in drug response. This review aims to summarize the reported data on the impact of different gene-variants on drug response in SQTS and LQTS, as well as discuss the potential mechanisms by which gene-variants alter drug response. These findings may provide valuable information for future studies on the influence of gene variants on drug efficacy and the development of genotype-guided or precision treatment for these diseases.
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Affiliation(s)
- Zhihan Zhao
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Xiaobiao Zang
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Kerun Niu
- Department of Orthopaedic, Henan Provincial People's Hospital; Zhengzhou University People's Hospital, Zhengzhou, Henan, 450003, China
| | - Weifeng Song
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Xianqing Wang
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Andreas Mügge
- Department of Cardiology and Angiology, Bergmannsheil University Hospitals, Ruhr University of Bochum, 44789, Bochum, Germany
| | - Assem Aweimer
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty and Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany
| | - Nazha Hamdani
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty and Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany
- HCEMM-Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, University of Budapest, Budapest, Hungary
- Department of Physiology, Cardiovascular Research Institute Maastricht University Maastricht, Maastricht, the Netherlands
| | - Xiaobo Zhou
- Cardiology, Angiology, Haemostaseology, and Medical Intensive Care, Medical Centre Mannheim, Medical Faculty Mannheim, Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site Heidelberg/Mannheim, Medical Centre Mannheim, Heidelberg University, Germany
- Key Laboratory of Medical Electrophysiology of Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China
| | - Yonghui Zhao
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Ibrahim Akin
- Cardiology, Angiology, Haemostaseology, and Medical Intensive Care, Medical Centre Mannheim, Medical Faculty Mannheim, Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site Heidelberg/Mannheim, Medical Centre Mannheim, Heidelberg University, Germany
| | - Ibrahim El-Battrawy
- Department of Cardiology and Angiology, Bergmannsheil University Hospitals, Ruhr University of Bochum, 44789, Bochum, Germany
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty and Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany
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3
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Serbus LR. A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging. Methods Mol Biol 2024; 2739:349-373. [PMID: 38006562 DOI: 10.1007/978-1-0716-3553-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.
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Affiliation(s)
- Laura Renee Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
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4
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Krueger TD, Chen C, Fang C. Targeting Ultrafast Spectroscopic Insights into Red Fluorescent Proteins. Chem Asian J 2023; 18:e202300668. [PMID: 37682793 DOI: 10.1002/asia.202300668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/10/2023]
Abstract
Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs across the imaging and life sciences. Since the rational design of RFPs with improved functions or enhanced versatility requires a mechanistic understanding of their working mechanisms, while fluorescence is intrinsically an ultrafast event, a suitable toolset involving steady-state and time-resolved spectroscopic techniques has become powerful in delineating key structural features and dynamic steps which govern irreversible photoconverting or reversible photoswitching RFPs, and large Stokes shift (LSS)RFPs. The pertinent cis-trans isomerization and protonation state change of RFP chromophores in their local environments, involving key residues in protein matrices, lead to rich and complicated spectral features across multiple timescales. In particular, ultrafast excited-state proton transfer in various LSSRFPs showcases the resolving power of wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in mapping a photocycle with crucial knowledge about the red-emitting species. Moreover, recent progress in noncanonical RFPs with a site-specifically modified chromophore provides an appealing route for efficient engineering of redder and brighter RFPs, highly desirable for bioimaging. Such an effective feedback loop involving physical chemists, protein engineers, and biomedical microscopists will enable future successes to expand fundamental knowledge and improve human health.
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Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
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5
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Le T, Chiang Y, Hui Y, Le T, Tzeng Y, Sharma N, Chiang W, Hsiao W. In vitroBioimaging of Fluorescent Nanodiamonds. NANODIAMONDS IN ANALYTICAL AND BIOLOGICAL SCIENCES 2023:95-127. [DOI: 10.1002/9781394202164.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
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6
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Joron K, Viegas JO, Haas-Neill L, Bier S, Drori P, Dvir S, Lim PSL, Rauscher S, Meshorer E, Lerner E. Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation. Nat Commun 2023; 14:4885. [PMID: 37573411 PMCID: PMC10423231 DOI: 10.1038/s41467-023-40647-6] [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: 01/19/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.
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Affiliation(s)
- Khalil Joron
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Juliane Oliveira Viegas
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Liam Haas-Neill
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Sariel Bier
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Shani Dvir
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Patrick Siang Lin Lim
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Sarah Rauscher
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
- Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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7
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Gu N, Chen C, Kabeya Y, Hasebe M, Tamada Y. Topoisomerase 1α is required for synchronous spermatogenesis in Physcomitrium patens. THE NEW PHYTOLOGIST 2022; 234:137-148. [PMID: 35067949 DOI: 10.1111/nph.17983] [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: 11/04/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
DNA topoisomerase 1 (TOP1) plays general roles in DNA replication and transcription by regulating DNA topology in land plants and metazoans. TOP1 is also involved in specific developmental events; however, whether TOP1 plays a conserved developmental role among multicellular organisms is unknown. Here, we investigated the developmental roles of TOP1 in the moss Physcomitrium (Physcomitrella) patens with gene targeting, microscopy, 3D image segmentation and crossing experiments. We discovered that the disruption of TOP1α, but not its paralogue TOP1β, leads to a defect in fertilisation and subsequent sporophyte formation in P. patens. In the top1α mutant, the egg cell was functional for fertilisation, while sperm cells were fewer and infertile with disordered structures. We observed that the nuclei volume of wild-type sperm cells synchronously decreases during antheridium development, indicating chromatin condensation towards the compact sperm head. By contrast, the top1α mutant exhibited attenuated cell divisions and asynchronous and defective contraction of the nuclei of sperm cells throughout spermatogenesis. These results indicate that TOP1α is involved in cell division and chromatin condensation during spermatogenesis in P. patens. Our results suggest that the regulation of DNA topology by TOP1 plays a key role in spermatogenesis in both land plants and metazoans.
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Affiliation(s)
- Nan Gu
- Robotics, Engineering and Agriculture-technology Laboratory (REAL), Utsunomiya University, Utsunomiya, 321-8585, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, 321-8585, Japan
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Chunli Chen
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang, 550025, China
| | - Yukiko Kabeya
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, 444-8585, Japan
| | - Yosuke Tamada
- Robotics, Engineering and Agriculture-technology Laboratory (REAL), Utsunomiya University, Utsunomiya, 321-8585, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, 321-8585, Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, 444-8585, Japan
- Center for Optical Research & Education (CORE), Utsunomiya University, Utsunomiya, 321-8585, Japan
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8
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Storti B, Carlotti B, Chiellini G, Ruglioni M, Salvadori T, Scotto M, Elisei F, Diaspro A, Bianchini P, Bizzarri R. An Efficient Aequorea victoria Green Fluorescent Protein for Stimulated Emission Depletion Super-Resolution Microscopy. Int J Mol Sci 2022; 23:ijms23052482. [PMID: 35269626 PMCID: PMC8910729 DOI: 10.3390/ijms23052482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
In spite of their value as genetically encodable reporters for imaging in living systems, fluorescent proteins have been used sporadically for stimulated emission depletion (STED) super-resolution imaging, owing to their moderate photophysical resistance, which does not enable reaching resolutions as high as for synthetic dyes. By a rational approach combining steady-state and ultrafast spectroscopy with gated STED imaging in living and fixed cells, we here demonstrate that F99S/M153T/V163A GFP (c3GFP) represents an efficient genetic reporter for STED, on account of no excited state absorption at depletion wavelengths <600 nm and a long emission lifetime. This makes c3GFP a valuable alternative to more common, but less photostable, EGFP and YFP/Citrine mutants for STED imaging studies targeting the green-yellow region of the optical spectrum.
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Affiliation(s)
- Barbara Storti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Correspondence:
| | - Benedetta Carlotti
- Department of Chemistry, Biology and Biotechnology and CEMIN, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy; (B.C.); (F.E.)
| | - Grazia Chiellini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Martina Ruglioni
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Tiziano Salvadori
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Marco Scotto
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and CEMIN, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy; (B.C.); (F.E.)
| | - Alberto Diaspro
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
- DIFILAB, Dipartimento di Fisica, Università degli Studi di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Paolo Bianchini
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
| | - Ranieri Bizzarri
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
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9
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Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
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10
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Kay TM, Aplin CP, Simonet R, Beenken J, Miller RC, Libal C, Boersma AJ, Sheets ED, Heikal AA. Molecular Brightness Approach for FRET Analysis of Donor-Linker-Acceptor Constructs at the Single Molecule Level: A Concept. Front Mol Biosci 2021; 8:730394. [PMID: 34595208 PMCID: PMC8476790 DOI: 10.3389/fmolb.2021.730394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In this report, we have developed a simple approach using single-detector fluorescence autocorrelation spectroscopy (FCS) to investigate the Förster resonance energy transfer (FRET) of genetically encoded, freely diffusing crTC2.1 (mTurquoise2.1-linker-mCitrine) at the single molecule level. We hypothesize that the molecular brightness of the freely diffusing donor (mTurquoise2.1) in the presence of the acceptor (mCitrine) is lower than that of the donor alone due to FRET. To test this hypothesis, the fluorescence fluctuation signal and number of molecules of freely diffusing construct were measured using FCS to calculate the molecular brightness of the donor, excited at 405 nm and detected at 475/50 nm, in the presence and absence of the acceptor. Our results indicate that the molecular brightness of cleaved crTC2.1 in a buffer is larger than that of the intact counterpart under 405-nm excitation. The energy transfer efficiency at the single molecule level is larger and more spread in values as compared with the ensemble-averaging time-resolved fluorescence measurements. In contrast, the molecular brightness of the intact crTC2.1, under 488 nm excitation of the acceptor (531/40 nm detection), is the same or slightly larger than that of the cleaved counterpart. These FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of the precise time constants associated with autocorrelation curves due to the presence of potential photophysical processes. Ultimately, when used in living cells, the proposed approach would only require a low expression level of these genetically encoded constructs, helping to limit potential interference with the cell machinery.
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Affiliation(s)
- Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN, United States
| | - Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Rowan Simonet
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Julie Beenken
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Christin Libal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
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11
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Aplin CP, Miller RC, Kay TM, Heikal AA, Boersma AJ, Sheets ED. Fluorescence depolarization dynamics of ionic strength sensors using time-resolved anisotropy. Biophys J 2021; 120:1417-1430. [PMID: 33582140 DOI: 10.1016/j.bpj.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/17/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022] Open
Abstract
Eukaryotic cells exploit dynamic and compartmentalized ionic strength to impact a myriad of biological functions such as enzyme activities, protein-protein interactions, and catalytic functions. Herein, we investigated the fluorescence depolarization dynamics of recently developed ionic strength biosensors (mCerulean3-linker-mCitrine) in Hofmeister salt (KCl, NaCl, NaI, and Na2SO4) solutions. The mCerulean3-mCitrine acts as a Förster resonance energy transfer (FRET) pair, tethered together by two oppositely charged α-helices in the linker region. We developed a time-resolved fluorescence depolarization anisotropy approach for FRET analyses, in which the donor (mCerulean3) is excited by 425-nm laser pulses, followed by fluorescence depolarization analysis of the acceptor (mCitrine) in KE (lysine-glutamate), arginine-aspartate, and arginine-glutamate ionic strength sensors with variable amino acid sequences. Similar experiments were carried out on the cleaved sensors as well as an E6G2 construct, which has neutral α-helices in the linker region, as a control. Our results show distinct dynamics of the intact and cleaved sensors. Importantly, the FRET efficiency decreases and the donor-acceptor distance increases as the environmental ionic strength increases. Our chemical equilibrium analyses of the collapsed-to-stretched conformational state transition of KE reveal that the corresponding equilibrium constant and standard Gibbs free energy changes are ionic strength dependent. We also tested the existing theoretical models for FRET analyses using steady-state anisotropy, which reveal that the angle between the dipole moments of the donor and acceptor in the KE sensor are sensitive to the ionic strength. These results help establish the time-resolved depolarization dynamics of these genetically encoded donor-acceptor pairs as a quantitative means for FRET analysis, which complement traditional methods such as time-resolved fluorescence for future in vivo studies.
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Affiliation(s)
- Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, Minnesota
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota.
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany.
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota.
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12
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Antonescu ON, Rasmussen A, Damm NAM, Heidemann DF, Popov R, Nesterov-Mueller A, Johansson KE, Winther JR. Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays. PLoS One 2021; 16:e0241461. [PMID: 33534832 PMCID: PMC7857580 DOI: 10.1371/journal.pone.0241461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 11/23/2022] Open
Abstract
Split fluorescent proteins have wide applicability as biosensors for protein-protein interactions, genetically encoded tags for protein detection and localization, as well as fusion partners in super-resolution microscopy. We have here established and validated a novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) in high throughput and with rapid turnover. We have screened more than 12,000 variants of the beta-strand split fragment using high-density peptide microarrays for binding and functional complementation in Green Fluorescent Protein. We studied the effect of peptide length and the effect of different linkers to the solid support. We further mapped the effect of all possible amino acid substitutions on each position as well as in the context of some single and double amino acid substitutions. As all peptides were tested in 12 duplicates, the analysis rests on a firm statistical basis allowing for confirmation of the robustness and precision of the method. Based on experiments in solution, we conclude that under the given conditions, the signal intensity on the peptide microarray faithfully reflects the binding affinity between the split fragments. With this, we are able to identify a peptide with 9-fold higher affinity than the starting peptide.
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Affiliation(s)
- Oana N. Antonescu
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Andreas Rasmussen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Nicole A. M. Damm
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Ditte F. Heidemann
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Kristoffer E. Johansson
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Jakob R. Winther
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
- * E-mail:
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13
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Kim N, Shin S, Bae SW. cAMP Biosensors Based on Genetically Encoded Fluorescent/Luminescent Proteins. BIOSENSORS-BASEL 2021; 11:bios11020039. [PMID: 33572585 PMCID: PMC7911721 DOI: 10.3390/bios11020039] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Cyclic adenosine monophosphate (cAMP) plays a key role in signal transduction pathways as a second messenger. Studies on the cAMP dynamics provided useful scientific insights for drug development and treatment of cAMP-related diseases such as some cancers and prefrontal cortex disorders. For example, modulation of cAMP-mediated intracellular signaling pathways by anti-tumor drugs could reduce tumor growth. However, most early stage tools used for measuring the cAMP level in living organisms require cell disruption, which is not appropriate for live cell imaging or animal imaging. Thus, in the last decades, tools were developed for real-time monitoring of cAMP distribution or signaling dynamics in a non-invasive manner. Genetically-encoded sensors based on fluorescent proteins and luciferases could be powerful tools to overcome these drawbacks. In this review, we discuss the recent genetically-encoded cAMP sensors advances, based on single fluorescent protein (FP), Föster resonance energy transfer (FRET), single luciferase, and bioluminescence resonance energy transfer (BRET) for real-time non-invasive imaging.
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Affiliation(s)
- Namdoo Kim
- Department of Chemistry, Kongju National University, Gongju 32588, Korea;
| | - Seunghan Shin
- Green Chemistry & Materials Group, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea;
| | - Se Won Bae
- Green Chemistry & Materials Group, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea;
- Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Korea
- Correspondence: ; Tel.: +82-64-754-3543
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14
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Sivaguru M, Todorov LG, Miller CAH, Fouke CE, Munro CMO, Fouke KW, Fouke KE, Baughman ME, Fouke BW. Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature. Sci Rep 2021; 11:2230. [PMID: 33500473 PMCID: PMC7838310 DOI: 10.1038/s41598-021-81520-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Lauren G Todorov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carly A H Miller
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Courtney E Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, Denison University, Granville, OH, USA
| | - Cara M O Munro
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Ecology and Evolutionary Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Kyle W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kaitlyn E Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, Denison University, Granville, OH, USA
- The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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15
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Basak S, Sakia N, Dougherty L, Guo Z, Wu F, Mindlin F, Lary JW, Cole JL, Ding F, Bowen ME. Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer. J Mol Biol 2021; 433:166793. [PMID: 33388290 DOI: 10.1016/j.jmb.2020.166793] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022]
Abstract
Many proteins are composed of independently-folded domains connected by flexible linkers. The primary sequence and length of such linkers can set the effective concentration for the tethered domains, which impacts rates of association and enzyme activity. The length of such linkers can be sensitive to environmental conditions, which raises questions as to how studies in dilute buffer relate to the highly-crowded cellular environment. To examine the role of linkers in domain separation, we measured Fluorescent Protein-Fluorescence Resonance Energy Transfer (FP-FRET) for a series of tandem FPs that varied in the length of their interdomain linkers. We used discrete molecular dynamics to map the underlying conformational distribution, which revealed intramolecular contact states that we confirmed with single molecule FRET. Simulations found that attached FPs increased linker length and slowed conformational dynamics relative to the bare linkers. This makes the CLYs poor sensors of inherent linker properties. However, we also showed that FP-FRET in CLYs was sensitive to solvent quality and macromolecular crowding making them potent environmental sensors. Finally, we targeted the same proteins to the plasma membrane of living mammalian cells to measure FP-FRET in cellulo. The measured FP-FRET when tethered to the plasma membrane was the same as that in dilute buffer. While caveats remain regarding photophysics, this suggests that the supertertiary conformational ensemble of these CLY proteins may not be affected by this specific cellular environment.
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Affiliation(s)
- Sujit Basak
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Nabanita Sakia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634-0978, USA
| | - Laura Dougherty
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Zhuojun Guo
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Fang Wu
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Frank Mindlin
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Jeffrey W Lary
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, CT 06269, USA
| | - James L Cole
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, CT 06269, USA; Department of Molecular and Cell Biology, and Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634-0978, USA
| | - Mark E Bowen
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA.
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16
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Golonka D, Gerken U, Köhler J, Möglich A. The Association Kinetics Encode the Light Dependence of Arabidopsis Phytochrome B Interactions. J Mol Biol 2020; 432:4327-4340. [PMID: 32534065 DOI: 10.1016/j.jmb.2020.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 01/18/2023]
Abstract
Plant phytochromes enable vital adaptations to red and far-red light. At the molecular level, these responses are mediated by light-regulated interactions between phytochromes and partner proteins, foremost the phytochrome-interacting factors (PIF). Although known for decades, quantitative analyses of these interactions have long been sparse. To address this deficit, we here studied by an integrated fluorescence-spectroscopic approach the equilibrium and kinetics of Arabidopsis thaliana phytochrome B binding to a tetramerized PIF6 variant. Several readouts consistently showed the stringently light-regulated interaction to be little affected by PIF tetramerization. Analysis of the binding kinetics allowed the determination of bimolecular association and unimolecular dissociation rate constants as a function of light. Unexpectedly, the stronger affinity of A. thaliana phytochrome B under red light relative to far-red light is entirely due to accelerated association rather than decelerated dissociation. The association reaction under red light is highly efficient and only 3-fold slower than the diffusion limit. The present findings pertain equally to the analysis of signal transduction in plants and to the biotechnological application of phytochromes.
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Affiliation(s)
- David Golonka
- Lehrstuhl für Biochemie, Photobiochemie, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Uwe Gerken
- Lehrstuhl für Spektroskopie weicher Materie, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Jürgen Köhler
- Lehrstuhl für Spektroskopie weicher Materie, Universität Bayreuth, 95447 Bayreuth, Germany; Bayerisches Polymer Institut, Universität Bayreuth, 95447 Bayreuth, Germany; Bayreuther Institut für Makromolekülforschung, 95447 Bayreuth, Germany.
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Photobiochemie, Universität Bayreuth, 95447 Bayreuth, Germany; Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany.
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17
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Kumar M, Quan X, Awatsuji Y, Tamada Y, Matoba O. Digital Holographic Multimodal Cross-Sectional Fluorescence and Quantitative Phase Imaging System. Sci Rep 2020; 10:7580. [PMID: 32415184 PMCID: PMC7228964 DOI: 10.1038/s41598-020-64028-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/03/2020] [Indexed: 12/29/2022] Open
Abstract
We present a multimodal imaging system based on simple off-axis digital holography, for simultaneous recording and retrieval of cross-sectional fluorescence and quantitative phase imaging of the biological specimen. Synergism in the imaging capabilities can be achieved by incorporating two off-axis digital holographic microscopes integrated to record different information at the same time. The cross-sectional fluorescence imaging is realized by a common-path configuration of the single-shot off-axis incoherent digital holographic system. The quantitative phase imaging, on the other hand, is achieved by another off-axis coherent digital holographic microscopy operating in transmission mode. The fundamental characteristics of the proposed multimodal system are confirmed by performing various experiments on fluorescent beads and fluorescent protein-labeled living cells of the moss Physcomitrella patens lying at different axial depth positions. Furthermore, the cross-sectional live fluorescence and phase imaging of the fluorescent beads are demonstrated by the proposed multimodal system. The experimental results presented here corroborate the feasibility of the proposed system and indicate its potential in the applications to analyze the functional and structural behavior of biological cells and tissues.
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Affiliation(s)
- Manoj Kumar
- Graduate School of System Informatics, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan.
| | - Xiangyu Quan
- Graduate School of System Informatics, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Yasuhiro Awatsuji
- Faculty of Electrical Engineering and Electronics, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Yosuke Tamada
- School of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, 321-8585, Japan
- National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
- School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
- Center for Optical Research and Education (CORE), Utsunomiya University, 7-1-2 Yoto, Utsunomiya, 321-8585, Japan
| | - Osamu Matoba
- Graduate School of System Informatics, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan.
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18
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Kumar M, Quan X, Awatsuji Y, Cheng C, Hasebe M, Tamada Y, Matoba O. Common-path multimodal three-dimensional fluorescence and phase imaging system. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-15. [PMID: 32030941 PMCID: PMC7003711 DOI: 10.1117/1.jbo.25.3.032010] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 01/14/2020] [Indexed: 05/26/2023]
Abstract
<p>A stable multimodal system is developed by combining two common-path digital holographic microscopes (DHMs): coherent and incoherent, for simultaneous recording and retrieval of three-dimensional (3-D) phase and 3-D fluorescence imaging (FI), respectively, of a biological specimen. The 3-D FI is realized by a single-shot common-path off-axis fluorescent DHM developed recently by our group. In addition, we accomplish, the phase imaging by another single-shot, highly stable common-path off-axis DHM based on a beam splitter. In this DHM configuration, a beam splitter is used to divide the incoming object beam into two beams. One beam serves as the object beam carrying the useful information of the object under study, whereas another beam is spatially filtered at its Fourier plane by using a pinhole and it serves as a reference beam. This DHM setup, owing to a common-path geometry, is less vibration-sensitive and compact, having a similar field of view but with high temporal phase stability in comparison to a two-beam Mach-Zehnder-type DHM. The performance of the proposed common-path DHM and the multimodal system is verified by conducting various experiments on fluorescent microspheres and fluorescent protein-labeled living cells of the moss <italic>Physcomitrella patens</italic>. Moreover, the potential capability of the proposed multimodal system for 3-D live fluorescence and phase imaging of the fluorescent beads is also demonstrated. The obtained experimental results corroborate the feasibility of the proposed multimodal system and indicate its potential applications for the analysis of functional and structural behaviors of a biological specimen and enhancement of the understanding of physiological mechanisms and various biological diseases.</p>.
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Affiliation(s)
- Manoj Kumar
- Kobe University, Graduate School of System Informatics, Kobe, Japan
| | - Xiangyu Quan
- Kobe University, Graduate School of System Informatics, Kobe, Japan
| | - Yasuhiro Awatsuji
- Kyoto Institute of Technology, Faculty of Electrical Engineering and Electronics, Kyoto, Japan
| | - Chaoyang Cheng
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, JST, Okazaki, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- ERATO, JST, Okazaki, Japan
- SOKENDAI (The Graduate University for Advanced Studies), School of Life Science, Okazaki, Japan
| | - Yosuke Tamada
- National Institute for Basic Biology, Okazaki, Japan
- SOKENDAI (The Graduate University for Advanced Studies), School of Life Science, Okazaki, Japan
- Utsunomiya University, School of Engineering, Utsunomiya, Japan
| | - Osamu Matoba
- Kobe University, Graduate School of System Informatics, Kobe, Japan
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19
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Castellani CM, Torres-Ocampo AP, Breffke J, White AB, Chambers JJ, Stratton MM, Maresca TJ. Live-cell FLIM-FRET using a commercially available system. Methods Cell Biol 2020; 158:63-89. [PMID: 32423651 PMCID: PMC8006575 DOI: 10.1016/bs.mcb.2020.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Förster resonance energy transfer (FRET)-based sensors have been powerful tools in cell biologists' toolkit for decades. Informed by fundamental understanding of fluorescent proteins, protein-protein interactions, and the structural biology of reporter components, researchers have been able to employ creative design approaches to build sensors that are uniquely capable of probing a wide range of phenomena in living cells including visualization of localized calcium signaling, sub-cellular activity gradients, and tension generation to name but a few. While FRET sensors have significantly impacted many fields, one must also be cognizant of the limitations to conventional, intensity-based FRET measurements stemming from variation in probe concentration, sensitivity to photobleaching, and bleed-through between the FRET fluorophores. Fluorescence lifetime imaging microscopy (FLIM) largely overcomes the limitations of intensity-based FRET measurements. In general terms, FLIM measures the time, which for the reporters described in this chapter is nanoseconds (ns), between photon absorption and emission by a fluorophore. When FLIM is applied to FRET sensors (FLIM-FRET), measurement of the donor fluorophore lifetime provides valuable information such as FRET efficiency and the percentage of reporters engaged in FRET. This chapter introduces fundamental principles of FLIM-FRET toward informing the practical application of the technique and, using two established FRET reporters as proofs of concept, outlines how to use a commercially available FLIM system.
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Affiliation(s)
| | - Ana P. Torres-Ocampo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
| | | | | | - James J. Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA
| | - Margaret M. Stratton
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
| | - Thomas J. Maresca
- Biology Department, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
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20
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Mystek P, Rysiewicz B, Gregrowicz J, Dziedzicka-Wasylewska M, Polit A. Gγ and Gα Identity Dictate a G-Protein Heterotrimer Plasma Membrane Targeting. Cells 2019; 8:E1246. [PMID: 31614907 PMCID: PMC6829862 DOI: 10.3390/cells8101246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/18/2022] Open
Abstract
Heterotrimeric G-proteins along with G-protein-coupled receptors (GPCRs) regulate many biochemical functions by relaying the information from the plasma membrane to the inside of the cell. The lipid modifications of Gα and Gγ subunits, together with the charged regions on the membrane interaction surface, provide a peculiar pattern for various heterotrimeric complexes. In a previous study, we found that Gαs and Gαi3 prefer different types of membrane-anchor and subclass-specific lipid domains. In the present report, we examine the role of distinct Gγ subunits in the membrane localization and spatiotemporal dynamics of Gαs and Gαi3 heterotrimers. We characterized lateral diffusion and G-protein subunit interactions in living cells using fluorescence recovery after photobleaching (FRAP) microscopy and fluorescence resonance energy transfer (FRET) detected by fluorescence lifetime imaging microscopy (FLIM), respectively. The interaction of Gγ subunits with specific lipids was confirmed, and thus the modulation of heterotrimeric G-protein localization. However, the Gα subunit also modulates trimer localization, and so the membrane distribution of heterotrimeric G-proteins is not dependent on Gγ only.
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Affiliation(s)
- Paweł Mystek
- Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Beata Rysiewicz
- Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Jan Gregrowicz
- Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Agnieszka Polit
- Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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21
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Shields RC, Kaspar JR, Lee K, Underhill SAM, Burne RA. Fluorescence Tools Adapted for Real-Time Monitoring of the Behaviors of Streptococcus Species. Appl Environ Microbiol 2019; 85:e00620-19. [PMID: 31101614 PMCID: PMC6643251 DOI: 10.1128/aem.00620-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/11/2019] [Indexed: 12/21/2022] Open
Abstract
Tagging of bacteria with fluorescent proteins has become an essential component of modern microbiology. Fluorescent proteins can be used to monitor gene expression and biofilm growth and to visualize host-pathogen interactions. Here, we developed a collection of fluorescent protein reporter plasmids for Streptococcus mutans UA159 and other oral streptococci. Using superfolder green fluorescent protein (sfGFP) as a reporter for transcriptional activity, we were able to characterize four strong constitutive promoters in S. mutans These promoter-sfgfp fusions worked both for single-copy chromosomal integration and on a multicopy plasmid, with the latter being segregationally stable in the absence of selective pressure under the conditions tested. We successfully labeled S. mutans UA159, Streptococcus gordonii DL1, and Streptococcus sp. strain A12 with sfGFP, DsRed-Express2 (red), and citrine (yellow). To test these plasmids under more challenging conditions, we performed mixed-species biofilm experiments and separated fluorescent populations using fluorescence-activated cell sorting (FACS). This allowed us to visualize two streptococci at a time and quantify the amounts of each species simultaneously. These fluorescent reporter plasmids add to the genetic toolbox available for the study of oral streptococci.IMPORTANCE Oral streptococci are the most abundant bacteria in the mouth and have a major influence on oral health and disease. In this study, we designed and optimized the expression of fluorescent proteins in Streptococcus mutans and other oral streptococci. We monitored the levels of expression and noise (the variability in fluorescence across the population). We then created several fluorescent protein delivery systems (green, yellow, and red) for use in oral streptococci. The data show that we can monitor bacterial growth and interactions in situ, differentiating between different bacteria growing in biofilms, the natural state of the organisms in the human mouth. These new tools will allow researchers to study these bacteria in novel ways to create more effective diagnostic and therapeutic tools for ubiquitous infectious diseases.
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Affiliation(s)
- R C Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - J R Kaspar
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - K Lee
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - S A M Underhill
- Department of Physics, University of Florida, Gainesville, Florida, USA
| | - R A Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
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22
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Schwarz J, J Leopold H, Leighton R, Miller RC, Aplin CP, Boersma AJ, Heikal AA, Sheets ED. Macromolecular crowding effects on energy transfer efficiency and donor-acceptor distance of hetero-FRET sensors using time-resolved fluorescence. Methods Appl Fluoresc 2019; 7:025002. [PMID: 30690439 DOI: 10.1088/2050-6120/ab0242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Living cells are crowded with macromolecules and organelles, which affect a myriad of biochemical processes. As a result, there is a need for sensitive molecular sensors for quantitative, site-specific assessment of macromolecular crowding. Here, we investigated the excited-state dynamics of recently developed hetero-FRET sensors (mCerulean3-linker-mCitrine) in homogeneous and heterogeneous environments using time-resolved fluorescence measurements, which are compatible with fluorescence lifetime imaging microscopy (FLIM). The linker in these FRET constructs, which tether the mCerulean3 (the donor) and mCitrine (the acceptor), vary in both length and flexibility. Glycerol and Ficoll-70 solutions were used for homogeneous and heterogeneous environments, respectively, at variable concentrations. The wavelength-dependent studies suggest that the 425-nm excitation and the 475-nm emission of the donor are best suited for quantitative assessment of the energy transfer efficiency and the donor-acceptor distance of these FRET probes. Under the same experimental conditions, the enzymatically cleaved counterpart of these probes was used as a control as well as a means to account for the changes in the environmental refractive indices. Our results indicate that the energy transfer efficiency of these FRET probes increases as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor a compact structure with enhanced energy transfer efficiency and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the stretched conformation of these FRET probes is more favorable in the viscous, homogeneous environment with a reduced energy transfer efficiency and relatively larger donor-acceptor distance as compared with those in pure buffer, which was attributed to a reduced structural fluctuation of the mCerulean3-mCitrine FRET pair in the viscous, more restrictive glycerol-enriched buffer. Our findings will help to advance the potential of these hetero-FRET probes using FLIM for spatio-temporal assessment of the compartmentalized crowding in living cells.
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Affiliation(s)
- Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN, United States of America
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23
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Yun CK, Hwang JW, Kwak TJ, Chang WJ, Ha S, Han K, Lee S, Choi YS. Nanoinjection system for precise direct delivery of biomolecules into single cells. LAB ON A CHIP 2019; 19:580-588. [PMID: 30623953 DOI: 10.1039/c8lc00709h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Intracellular delivery of functional molecules such as proteins, transcription factors and DNA is effective and promising in cell biology. However, existing transfection methods are often unsuitable to deliver big molecules into cells or require carriers such as viruses and peptides specific to the target molecules. In addition, the nature of bulk processing does not generally provide accurate dose control of individual cells. The concept of single-cell-based material injection based on electrokinetic pumping through nanocapillaries could overcome these problems, yet the fabrication and operation of nanoscale 3-dimensional structures have remained unsolved. In this research, a hybrid (PDMS/glass) microfluidic chip with a true 3-dimensional nanoinjection structure (called "nanoinjection system") is presented. The nanoinjection structure was fabricated by femtosecond-laser (fs-laser) ablation in a single solid glass, which showed very successful delivery of red fluorescent protein (RFP) and expression of plasmid DNA in several different types of cells. This system is promising in that the amount of molecules to be delivered is controllable and the processed cells are systematically separated into a harvesting chamber, which can radically improve the purity of the processed cells. In addition, it was confirmed that the cells were healthy even after the molecule injection for a few seconds, indicating that the injection time can be significantly elongated, further improving the delivery efficiency of biomolecules without affecting the cell viability. We envision that the nanoinjection system having the major features of being carrier-free and dose-controllable, having an unlimited injection period, and ease of harvesting will greatly contribute to the next-generation research studies in the fields of cell biology and cell therapeutics.
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Affiliation(s)
- Chang-Koo Yun
- Department of Biotechnology, CHA University, 335 Pankyoro, Bundang-gu, Seongnam, Gyeonggi-do 13488, Republic of Korea. and Department of Mechanical Engineering, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Jung Wook Hwang
- Department of Biotechnology, CHA University, 335 Pankyoro, Bundang-gu, Seongnam, Gyeonggi-do 13488, Republic of Korea.
| | - Tae Joon Kwak
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Woo-Jin Chang
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Sungjae Ha
- Femtobiomed Inc., Seongnam, 13487, Republic of Korea.
| | - Kyuboem Han
- Paean Biotechnology Inc., Daejeon, 34028, Republic of Korea
| | - Sanghyun Lee
- Femtobiomed Inc., Seongnam, 13487, Republic of Korea.
| | - Yong-Soo Choi
- Department of Biotechnology, CHA University, 335 Pankyoro, Bundang-gu, Seongnam, Gyeonggi-do 13488, Republic of Korea.
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24
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Ziegler CS, Bouchab L, Tramier M, Durand D, Fieschi F, Dupré-Crochet S, Mérola F, Nüße O, Erard M. Quantitative live-cell imaging and 3D modeling reveal critical functional features in the cytosolic complex of phagocyte NADPH oxidase. J Biol Chem 2019; 294:3824-3836. [PMID: 30630949 DOI: 10.1074/jbc.ra118.006864] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/08/2019] [Indexed: 01/18/2023] Open
Abstract
Phagocyte NADPH oxidase produces superoxide anions, a precursor of reactive oxygen species (ROS) critical for host responses to microbial infections. However, uncontrolled ROS production contributes to inflammation, making NADPH oxidase a major drug target. It consists of two membranous (Nox2 and p22phox) and three cytosolic subunits (p40phox, p47phox, and p67phox) that undergo structural changes during enzyme activation. Unraveling the interactions between these subunits and the resulting conformation of the complex could shed light on NADPH oxidase regulation and help identify inhibition sites. However, the structures and the interactions of flexible proteins comprising several well-structured domains connected by intrinsically disordered protein segments are difficult to investigate by conventional techniques such as X-ray crystallography, NMR, or cryo-EM. Here, we developed an analytical strategy based on FRET-fluorescence lifetime imaging (FLIM) and fluorescence cross-correlation spectroscopy (FCCS) to structurally and quantitatively characterize NADPH oxidase in live cells. We characterized the inter- and intramolecular interactions of its cytosolic subunits by elucidating their conformation, stoichiometry, interacting fraction, and affinities in live cells. Our results revealed that the three subunits have a 1:1:1 stoichiometry and that nearly 100% of them are present in complexes in living cells. Furthermore, combining FRET data with small-angle X-ray scattering (SAXS) models and published crystal structures of isolated domains and subunits, we built a 3D model of the entire cytosolic complex. The model disclosed an elongated complex containing a flexible hinge separating two domains ideally positioned at one end of the complex and critical for oxidase activation and interactions with membrane components.
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Affiliation(s)
- Cornelia S Ziegler
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Leïla Bouchab
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Marc Tramier
- the Université Rennes, CNRS, Institut de Génétique et Développement de Rennes - UMR 6290, BIOSIT - UMS 3480, F-35000 Rennes, France
| | - Dominique Durand
- the Institute for Integrative Biology of the Cell, CEA, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France, and
| | - Franck Fieschi
- the Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Sophie Dupré-Crochet
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Fabienne Mérola
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Oliver Nüße
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France,
| | - Marie Erard
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France,
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25
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Ghosh A, Karedla N, Thiele JC, Gregor I, Enderlein J. Fluorescence lifetime correlation spectroscopy: Basics and applications. Methods 2018; 140-141:32-39. [DOI: 10.1016/j.ymeth.2018.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022] Open
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26
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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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27
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Chen F, Zhao X, Liang W. One- and two-photon absorption spectra of the yellow fluorescent protein citrine: effects of intramolecular electron-vibrational coupling and intermolecular interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1426130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fasheng Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xinyi Zhao
- Department of Science and Technology for Inspection, Xiamen Huaxia University, Xiamen, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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28
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Heidarinejad M, Nakamura H, Inoue T. Stimulation-induced changes in diffusion and structure of calmodulin and calmodulin-dependent protein kinase II proteins in neurons. Neurosci Res 2018; 136:13-32. [PMID: 29395358 DOI: 10.1016/j.neures.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 11/28/2022]
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) and calmodulin (CaM) play essential roles in synaptic plasticity, which is an elementary process of learning and memory. In this study, fluorescence correlation spectroscopy (FCS) revealed diffusion properties of CaM, CaMKIIα and CaMKIIβ proteins in human embryonic kidney 293 (HEK293) cells and hippocampal neurons. A simultaneous multiple-point FCS recording system was developed on a random-access two-photon microscope, which facilitated efficient analysis of molecular dynamics in neuronal compartments. The diffusion of CaM in neurons was slower than that in HEK293 cells at rest, while the diffusion in stimulated neurons was accelerated and indistinguishable from that in HEK293 cells. This implied that activity-dependent binding partners of CaM exist in neurons, which slow down the diffusion at rest. Diffusion properties of CaMKIIα and β proteins implied that major populations of these proteins exist as holoenzymatic forms. Upon stimulation of neurons, the diffusion of CaMKIIα and β proteins became faster with reduced particle brightness, indicating drastic structural changes of the proteins such as dismissal from holoenzyme structure and further fragmentation.
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Affiliation(s)
- Morteza Heidarinejad
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Hideki Nakamura
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Takafumi Inoue
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
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29
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Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA. Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments. Phys Chem Chem Phys 2018; 20:24045-24057. [DOI: 10.1039/c8cp03873b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.
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Affiliation(s)
- Hong Bok Lee
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Anh Cong
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Hannah Leopold
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Megan Currie
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | | | - Erin D. Sheets
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Ahmed A. Heikal
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
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30
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Ghosh A, Isbaner S, Veiga-Gutiérrez M, Gregor I, Enderlein J, Karedla N. Quantifying Microsecond Transition Times Using Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem Lett 2017; 8:6022-6028. [PMID: 29183125 DOI: 10.1021/acs.jpclett.7b02707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many complex luminescent emitters such as fluorescent proteins exhibit multiple emitting states that result in rapid fluctuations of their excited-state lifetime. Here, we apply fluorescence lifetime correlation spectroscopy (FLCS) to resolve the photophysical state dynamics of the prototypical fluorescence protein enhanced green fluorescent protein (EGFP). We quantify the microsecond transition rates between its two fluorescent states, which have otherwise highly overlapping emission spectra. We relate these transitions to a room-temperature angstrom-scale rotational isomerism of an amino acid next to its fluorescent center. With this study, we demonstrate the power of FLCS for studying the rapid transition dynamics of a broad range of light-emitting systems with complex multistate photophysics, which cannot be easily done by other methods.
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Affiliation(s)
- Arindam Ghosh
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | - Sebastian Isbaner
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | | | - Ingo Gregor
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | - Narain Karedla
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
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31
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The Role of Probe Photophysics in Localization-Based Superresolution Microscopy. Biophys J 2017; 113:2037-2054. [PMID: 29117527 DOI: 10.1016/j.bpj.2017.08.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 01/03/2023] Open
Abstract
Fluorescent proteins are used extensively for biological imaging applications; photoactivatable and photoconvertible fluorescent proteins (PAFPs) are used widely in superresolution localization microscopy methods such as fluorescence photoactivation localization microscopy and photoactivated localization microscopy. However, their optimal use depends on knowledge of not only their bulk fluorescence properties, but also their photophysical properties at the single molecule level. We have used fluorescence correlation spectroscopy and cross-correlation spectroscopy to quantify the diffusion, photobleaching, fluorescence intermittency, and photoconversion dynamics of Dendra2, a well-known PAFP used in localization microscopy. Numerous dark states of Dendra2 are observed both in inactive (green fluorescent) and active (orange fluorescent) forms; the interconversion rates are both light- and pH-dependent, as observed for other PAFPs. The dark states limit the detected count rate per molecule, which is a crucial parameter for localization microscopy. We then developed, to our knowledge, a new mathematical estimate for the resolution in localization microscopy as a function of the measured photophysical parameters of the probe such as photobleaching quantum yield, count rate per molecule, and intensity of saturation. The model was used to predict the dependence of resolution on acquisition parameters such as illumination intensity and time per frame, demonstrating an optimal set of acquisition parameters for a given probe for a variety of measures of resolution. The best possible resolution was then compared for Dendra2 and other widely used probes, including Alexa dyes and quantum dots. This work establishes a framework for determination of the best possible resolution using a localization microscope to image a particular fluorophore, and suggests that development of probes for use in superresolution localization microscopy must consider the count rate per molecule, the saturation intensity, the photobleaching yield, and, crucially, management of bright/dark state transitions, to optimize image resolution.
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32
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Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies. J Phys Chem B 2017; 121:5688-5698. [DOI: 10.1021/acs.jpcb.7b01306] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Megan Currie
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Hannah Leopold
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Jacob Schwarz
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Erin D. Sheets
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Ahmed A. Heikal
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
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33
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PKCα diffusion and translocation are independent of an intact cytoskeleton. Sci Rep 2017; 7:475. [PMID: 28352102 PMCID: PMC5428563 DOI: 10.1038/s41598-017-00560-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/03/2017] [Indexed: 01/04/2023] Open
Abstract
Translocation of cytosolic cPKC to the plasma membrane is a key event in their activation process but its exact nature is still unclear with particular dispute whether sole diffusion or additional active transport along the cell’s cytoskeleton contributes to cPKC’s dynamics. This was addressed by analyzing the recruitment behavior of PKCα while manipulating the cytoskeleton. Photolytic Ca2+ uncaging allowed us to quantify the kinetics of PKCα redistribution to the plasma membrane when fused to monomeric, dimeric and tetrameric fluorescence proteins. Results indicated that translocation kinetics were modulated by the state of oligomerization as expected for varying Stokes’ radii of the participating proteins. Following depolymerization of the microtubules and the actin filaments we found that Ca2+ induced membrane accumulation of PKCα was independent of the filamentous state of the cytoskeleton. Fusion of PKCα to the photo-convertible fluorescent protein Dendra2 enabled the investigation of PKCα-cytoskeleton interactions under resting conditions. Redistribution following spatially restricted photoconversion showed that the mobility of the fusion protein was independent of the state of the cytoskeleton. Our data demonstrated that in living cells neither actin filaments nor microtubules contribute to PKCα’s cytosolic mobility or Ca2+-induced translocation to the plasma membrane. Instead translocation is a solely diffusion-driven process.
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34
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Matsuda S, Harada K, Ito M, Takizawa M, Wongso D, Tsuboi T, Kitaguchi T. Generation of a cGMP Indicator with an Expanded Dynamic Range by Optimization of Amino Acid Linkers between a Fluorescent Protein and PDE5α. ACS Sens 2017; 2:46-51. [PMID: 28722423 DOI: 10.1021/acssensors.6b00582] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here we describe the development of a single fluorescent protein (FP)-based cGMP indicator, Green cGull, based on the cGMP binding domain from mouse phosphodiesterase 5α. The dynamic range of Green cGull was enhanced to a 7.5-fold fluorescence change upon cGMP binding by optimization of the amino acid linkers between the cGMP binding domain and FP. Green cGull has excitation and emission peaks at 498 and 522 nm, respectively, and specifically responds to cGMP in a dose-dependent manner. Live cell imaging analysis revealed that addition of a nitric oxide (NO) donor induced different cGMP kinetics and was cell-type dependent. We also found that the NO donor induced an increase of intracellular cGMP, while intracellular Ca2+ exhibited a complex profile, as revealed by dual-color imaging of cGMP and Ca2+. The results suggest that Green cGull sheds new light on understanding the complex interactions between various signaling molecules by multicolor imaging and that our systematic strategy for expanding the dynamic range of single-FP-based indicators is valuable to generate indicators for molecules of interest.
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Affiliation(s)
- Shogo Matsuda
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Kazuki Harada
- Department
of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Motoki Ito
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Mai Takizawa
- Department
of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Devina Wongso
- Cell
Signaling Group, Waseda Bioscience Research Institute in Singapore (WABIOS), 11 Biopolis Way #05-02 Helios, Singapore 138667, Singapore
| | - Takashi Tsuboi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
- Department
of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Tetsuya Kitaguchi
- Cell
Signaling Group, Waseda Bioscience Research Institute in Singapore (WABIOS), 11 Biopolis Way #05-02 Helios, Singapore 138667, Singapore
- Comprehensive
Research Organization, Waseda University, #304, Block 120-4, 513 Wasedatsurumaki-cho, Shinjuku, Tokyo 162-0041, Japan
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35
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Single amino acid replacement transforms mCherry to a far-red fluorescent protein. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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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: 178] [Impact Index Per Article: 22.3] [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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A Guide to Fluorescent Protein FRET Pairs. SENSORS 2016; 16:s16091488. [PMID: 27649177 PMCID: PMC5038762 DOI: 10.3390/s16091488] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022]
Abstract
Förster or fluorescence resonance energy transfer (FRET) technology and genetically encoded FRET biosensors provide a powerful tool for visualizing signaling molecules in live cells with high spatiotemporal resolution. Fluorescent proteins (FPs) are most commonly used as both donor and acceptor fluorophores in FRET biosensors, especially since FPs are genetically encodable and live-cell compatible. In this review, we will provide an overview of methods to measure FRET changes in biological contexts, discuss the palette of FP FRET pairs developed and their relative strengths and weaknesses, and note important factors to consider when using FPs for FRET studies.
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Kodama Y. Time Gating of Chloroplast Autofluorescence Allows Clearer Fluorescence Imaging In Planta. PLoS One 2016; 11:e0152484. [PMID: 27027881 PMCID: PMC4814121 DOI: 10.1371/journal.pone.0152484] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
Chloroplast, an organelle facilitating photosynthesis, exhibits strong autofluorescence, which is an undesired background signal that restricts imaging experiments with exogenous fluorophore in plants. In this study, the autofluorescence was characterized in planta under confocal laser microscopy, and it was found that the time-gated imaging technique completely eliminates the autofluorescence. As a demonstration of the technique, a clearer signal of fluorescent protein-tagged phototropin, a blue-light photoreceptor localized at the chloroplast periphery, was visualized in planta.
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Affiliation(s)
- Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321–8505, Japan
- * E-mail:
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39
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Probing of protein localization and shuttling in mitochondrial microcompartments by FLIM with sub-diffraction resolution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1290-1299. [PMID: 27016377 DOI: 10.1016/j.bbabio.2016.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/31/2022]
Abstract
The cell is metabolically highly compartmentalized. Especially, mitochondria host many vital reactions in their different microcompartments. However, due to their small size, these microcompartments are not accessible by conventional microscopy. Here, we demonstrate that time-correlated single-photon counting (TCSPC) fluorescence lifetime-imaging microscopy (FLIM) classifies not only mitochondria, but different microcompartments inside mitochondria. Sensor proteins in the matrix had a different lifetime than probes at membrane proteins. Localization in the outer and inner mitochondrial membrane could be distinguished by significant differences in the lifetime. The method was sensitive enough to monitor shifts in protein location within mitochondrial microcompartments. Macromolecular crowding induced by changes in the protein content significantly affected the lifetime, while oxidizing conditions or physiological pH changes had only marginal effects. We suggest that FLIM is a versatile and completive method to monitor spatiotemporal events in mitochondria. The sensitivity in the time domain allows for gaining substantial information about sub-mitochondrial localization overcoming diffraction limitation. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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40
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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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41
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Berardozzi R, Adam V, Martins A, Bourgeois D. Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins. J Am Chem Soc 2016; 138:558-65. [PMID: 26675944 DOI: 10.1021/jacs.5b09923] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoactivated localization microscopy (PALM) is a powerful technique to investigate cellular nanostructures quantitatively and dynamically. However, the use of PALM for molecular counting or single-particle tracking remains limited by the propensity of photoconvertible fluorescent protein markers (PCFPs) to repeatedly enter dark states. By designing the single mutants mEos2-A69T and Dendra2-T69A, we completely swapped the blinking behaviors of mEos2 and Dendra2, two popular PCFPs. We combined X-ray crystallography and single-molecule microscopy to show that blinking in mEos2 and Dendra2 is largely controlled by the orientation of arginine 66, a highly conserved residue in Anthozoan PCFPs. The Arg66 side-chain conformation affects the bleaching and the on-to-off transition quantum yields, as well as the fraction of molecules entering long-lived dark states, resulting in widely different apparent blinking behaviors that largely modulate the efficiency of current blinking correction procedures. The present work provides mechanistic insight into the complex photophysics of Anthozoan PCFPs and will facilitate future engineering of bright and low-blinking variants suitable for PALM.
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Affiliation(s)
- Romain Berardozzi
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Alexandre Martins
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
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Junghans C, Schmitt FJ, Vukojević V, Friedrich T. Diffusion behavior of the fluorescent proteins eGFP and Dreiklang in solvents of different viscosity monitored by fluorescence correlation spectroscopy. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/optof-2016-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractFluorescence correlation spectroscopy relies on temporal autocorrelation analysis of fluorescence intensity fluctuations that spontaneously arise in systems at equilibrium due to molecular motion and changes of state that cause changes in fluorescence, such as triplet state transition, photoisomerization and other photophysical transformations, to determine the rates of these processes. The stability of a fluorescent molecule against dark state conversion is of particular concern for chromophores intended to be used as reference tags for comparing diffusion processes on multiple time scales. In this work, we analyzed properties of two fluorescent proteins, the photoswitchable Dreiklang and its parental eGFP, in solvents of different viscosity to vary the diffusion time through the observation volume element by several orders of magnitude. In contrast to eGFP, Dreiklang undergoes a dark-state conversion on the time scale of tens to hundreds of microseconds under conditions of intense fluorescence excitation, which results in artificially shortened diffusion times if the diffusional motion through the observation volume is sufficiently slowed down. Such photophysical quenching processes have also been observed in FCS studies on other photoswitchable fluorescent proteins including Citrine, from which Dreiklang was derived by genetic engineering. This property readily explains the discrepancies observed previously between the diffusion times of eGFP- and Dreiklang-labeled plasma membrane protein complexes.
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Rai J, Pemmasani JK, Voronovsky A, Jensen IS, Manavalan A, Nyengaard JR, Golas MM, Sander B. Strep-tag II and Twin-Strep based cassettes for protein tagging by homologous recombination and characterization of endogenous macromolecular assemblies in Saccharomyces cerevisiae. Mol Biotechnol 2015; 56:992-1003. [PMID: 24969434 DOI: 10.1007/s12033-014-9778-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide sequences fused to a gene of interest facilitate the isolation of proteins or protein complexes from cell extracts. In the case of fluorescent protein tags, the tagged protein can be visually localized in living cells. To tag endogenous genes, PCR-based homologous recombination is a powerful approach used in the yeast Saccharomyces cerevisiae. This approach uses short, homologous DNA sequences that flank the tagging cassette to direct recombination. Here, we constructed a set of plasmids, whose sequences were optimized for codon usage in yeast, for Strep-tag II and Twin-Strep tagging in S. cerevisiae. Some plasmids also contain sequences encoding for a fluorescent protein followed by the purification tag. We demonstrate using the yeast pyruvate dehydrogenase (PDH) complex that these plasmids can be used to purify large protein complexes efficiently. We furthermore demonstrate that purification from the endogenous pool using the Strep-tag system results in functionally active complexes. Finally, using the fluorescent tags, we show that a kinase and a phosphatase involved in regulating the activity of the PDH complex localize in the cells' mitochondria. In conclusion, our cassettes can be used as tools for biochemical, functional, and structural analyses of endogenous multi-protein assemblies in yeast.
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Affiliation(s)
- Jay Rai
- Stereology and EM Laboratory, Department of Clinical Medicine, Institute of Clinical Medicine, Aarhus University, c/o Wilhelm Meyers Allé 3, Building 1233/1234, 8000, Aarhus C, Denmark
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44
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Tanimura A. Development and application of fluorescent protein-based indicators for live cell imaging. J Oral Biosci 2015. [DOI: 10.1016/j.job.2015.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Frey S, Görlich D. The Xenopus laevis Atg4B Protease: Insights into Substrate Recognition and Application for Tag Removal from Proteins Expressed in Pro- and Eukaryotic Hosts. PLoS One 2015; 10:e0125099. [PMID: 25923686 PMCID: PMC4414272 DOI: 10.1371/journal.pone.0125099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/20/2015] [Indexed: 01/01/2023] Open
Abstract
During autophagy, members of the ubiquitin-like Atg8 protein family get conjugated to phosphatidylethanolamine and act as protein-recruiting scaffolds on the autophagosomal membrane. The Atg4 protease produces mature Atg8 from C-terminally extended precursors and deconjugates lipid-bound Atg8. We now found that Xenopus laevis Atg4B (xAtg4B) is ideally suited for proteolytic removal of N-terminal tags from recombinant proteins. To implement this strategy, an Atg8 cleavage module is inserted in between tag and target protein. An optimized xAtg4B protease fragment includes the so far uncharacterized C-terminus, which crucially contributes to recognition of the Xenopus Atg8 homologs xLC3B and xGATE16. xAtg4B-mediated tag cleavage is very robust in solution or on-column, efficient at 4°C and orthogonal to TEV protease and the recently introduced proteases bdSENP1, bdNEDP1 and xUsp2. Importantly, xLC3B fusions are stable in wheat germ extract or when expressed in Saccharomyces cerevisiae, but cleavable by xAtg4B during or following purification. We also found that fusions to the bdNEDP1 substrate bdNEDD8 are stable in S. cerevisiae. In combination, or findings now provide a system, where proteins and complexes fused to xLC3B or bdNEDD8 can be expressed in a eukaryotic host and purified by successive affinity capture and proteolytic release steps.
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Affiliation(s)
- Steffen Frey
- Abteilung Zelluläre Logistik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
- * E-mail: (SF); (DG)
| | - Dirk Görlich
- Abteilung Zelluläre Logistik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
- * E-mail: (SF); (DG)
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Sun G, Guo M, Teh C, Korzh V, Bathe M, Wohland T. Bayesian model selection applied to the analysis of fluorescence correlation spectroscopy data of fluorescent proteins in vitro and in vivo. Anal Chem 2015; 87:4326-33. [PMID: 25815704 PMCID: PMC4430836 DOI: 10.1021/acs.analchem.5b00022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a powerful technique to investigate molecular dynamics with single molecule sensitivity. In particular, in the life sciences it has found widespread application using fluorescent proteins as molecularly specific labels. However, FCS data analysis and interpretation using fluorescent proteins remains challenging due to typically low signal-to-noise ratio of FCS data and correlated noise in autocorrelated data sets. As a result, naive fitting procedures that ignore these important issues typically provide similarly good fits for multiple competing models without clear distinction of which model is preferred given the signal-to-noise ratio present in the data. Recently, we introduced a Bayesian model selection procedure to overcome this issue with FCS data analysis. The method accounts for the highly correlated noise that is present in FCS data sets and additionally penalizes model complexity to prevent over interpretation of FCS data. Here, we apply this procedure to evaluate FCS data from fluorescent proteins assayed in vitro and in vivo. Consistent with previous work, we demonstrate that model selection is strongly dependent on the signal-to-noise ratio of the measurement, namely, excitation intensity and measurement time, and is sensitive to saturation artifacts. Under fixed, low intensity excitation conditions, physical transport models can unambiguously be identified. However, at excitation intensities that are considered moderate in many studies, unwanted artifacts are introduced that result in nonphysical models to be preferred. We also determined the appropriate fitting models of a GFP tagged secreted signaling protein, Wnt3, in live zebrafish embryos, which is necessary for the investigation of Wnt3 expression and secretion in development. Bayes model selection therefore provides a robust procedure to determine appropriate transport and photophysical models for fluorescent proteins when appropriate models are provided, to help detect and eliminate experimental artifacts in solution, cells, and in living organisms.
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Affiliation(s)
- Guangyu Sun
- Department of Chemistry, National University of Singapore, 117543 Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557 Singapore
| | - Ming Guo
- Laboratory for Computational Biology and Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cathleen Teh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673 Singapore
| | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673 Singapore
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Mark Bathe
- Laboratory for Computational Biology and Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thorsten Wohland
- Department of Chemistry, National University of Singapore, 117543 Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557 Singapore
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
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Manna P, Jimenez R. Time and frequency-domain measurement of ground-state recovery times in red fluorescent proteins. J Phys Chem B 2015; 119:4944-54. [PMID: 25781915 DOI: 10.1021/acs.jpcb.5b00950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The field of bioimaging and biosensors has been revolutionized by the discovery of fluorescent proteins (FPs) and their use in live cells. FPs are characterized with rich photodynamics due to the presence of nonfluorescent or dark states which are responsible for fluorescence intermittency or "blinking", which has been exploited in several localization-based super-resolution techniques that surpass the diffraction-limited resolution of conventional microscopy. Molecules that convert to these dark states recover to the ground states either spontaneously or upon absorption of another photon, depending on the particular FP and the structural transition that is involved. In this work, we demonstrate time- and frequency-domain methods for the measurement of the ground-state recovery (GSR) times of FPs both in live cells and in solutions. In the time-domain method, we excited the sample with millisecond pulses at varying dark times to obtain percent-recovery. In the frequency-domain method, dark-state hysteresis was employed to obtain the positive phase shift or "phase advance". We extracted the GSR time constants from our measurements using calculations and simulations based on a three-state model system. The GSR time constants of the red FPs studied in these experiments fall in the range from μs to msec time-scales. We find that the time- and frequency-domain techniques are complementary to each other. While accurate GSR times can be extracted from the time-domain technique, frequency-domain measurements are primarily sensitive to the rates of dark-state conversion (DSC) processes. A correlation between GSR times, DSC, and photobleaching rates for the red FPs mCherry, TagRFP-T, and Kriek were observed. These time- and frequency-domain methods can be used in high-throughput screening and sorting of FPs clones based on GSR time constant and photostability and will therefore be valuable for the development of new photoswitchable or photoactivatable FPs.
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Affiliation(s)
- Premashis Manna
- †Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
- ‡JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- †Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
- ‡JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
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Rea AC, Nasrallah JB. In vivo imaging of the S-locus receptor kinase, the female specificity determinant of self-incompatibility, in transgenic self-incompatible Arabidopsis thaliana. ANNALS OF BOTANY 2015; 115:789-805. [PMID: 25714818 PMCID: PMC4373290 DOI: 10.1093/aob/mcv008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/25/2014] [Accepted: 01/09/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS The S-locus receptor kinase (SRK), which is expressed in stigma epidermal cells, is responsible for the recognition and inhibition of 'self' pollen in the self-incompatibility (SI) response of the Brassicaceae. The allele-specific interaction of SRK with its cognate pollen coat-localized ligand, the S-locus cysteine-rich (SCR) protein, is thought to trigger a signalling cascade within the stigma epidermal cell that leads to the arrest of 'self' pollen at the stigma surface. In addition to the full-length signalling SRK receptor, stigma epidermal cells express two other SRK protein species that lack the kinase domain and whose role in the SI response is not understood: a soluble version of the SRK ectodomain designated eSRK and a membrane-tethered form designated tSRK. The goal of this study was to describe the sub-cellular distribution of the various SRK protein species in stigma epidermal cells as a prelude to visualizing receptor dynamics in response to SCR binding. METHODS The Arabidopsis lyrata SRKb variant was tagged with the Citrine variant of yellow fluorescent protein (cYFP) and expressed in A. thaliana plants of the C24 accession, which had been shown to exhibit a robust SI response upon transformation with the SRKb-SCRb gene pair. The transgenes used in this study were designed for differential production and visualization of the three SRK protein species in stigma epidermal cells. Transgenic stigmas were analysed by pollination assays and confocal microscopy. KEY RESULTS AND CONCLUSIONS Pollination assays demonstrated that the cYFP-tagged SRK proteins are functional and that the eSRK is not required for SI. Confocal microscopic analysis of cYFP-tagged SRK proteins in live stigma epidermal cells revealed the differential sub-cellular localization of the three SRK protein species but showed no evidence for redistribution of these proteins subsequent to incompatible pollination.
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Affiliation(s)
- Anne C Rea
- Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, NY 14850, USA
| | - June B Nasrallah
- Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, NY 14850, USA
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49
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Abstract
Multiple sclerosis is an autoimmune disease of the CNS resulting in degeneration of myelin sheaths and loss of oligodendrocytes, which means that protection and electrical insulation of axons and rapid signal propagation are impaired, leading to axonal damage and permanent disabilities. Partial replacement of lost oligodendrocytes and remyelination can occur as a result of activation and recruitment of resident oligodendroglial precursor cells. However, the overall remyelination capacity remains inefficient because precursor cells often fail to generate new oligodendrocytes. Increasing evidence points to the existence of several molecular inhibitors that act on these cells and interfere with their cellular maturation. The p57kip2 gene encodes one such potent inhibitor of oligodendroglial differentiation and this study sheds light on the underlying mode of action. We found that subcellular distribution of the p57kip2 protein changed during differentiation of rat, mouse, and human oligodendroglial cells both in vivo and in vitro. Nuclear export of p57kip2 was correlated with promoted myelin expression, higher morphological phenotypes, and enhanced myelination in vitro. In contrast, nuclear accumulation of p57kip2 resulted in blocked oligodendroglial differentiation. Experimental evidence suggests that the inhibitory role of p57kip2 depends on specific interactions with binding proteins such as LIMK-1, CDK2, Mash1, and Hes5 either by controlling their site of action or their activity. Because functional restoration in demyelinating diseases critically depends on the successful generation of oligodendroglial cells, a therapeutic need that is currently unmet, the regulatory mechanism described here might be of particular interest for identifying suitable drug targets and devising novel therapeutic approaches.
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50
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Dean KM, Lubbeck JL, Davis LM, Regmi CK, Chapagain PP, Gerstman BS, Jimenez R, Palmer AE. Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. Integr Biol (Camb) 2015; 7:263-73. [PMID: 25477249 PMCID: PMC4323946 DOI: 10.1039/c4ib00251b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fluorescent proteins offer exceptional labeling specificity in living cells and organisms. Unfortunately, their photophysical properties remain far from ideal for long-term imaging of low-abundance cellular constituents, in large part because of their poor photostability. Despite widespread engineering efforts, improving the photostability of fluorescent proteins remains challenging due to lack of appropriate high-throughput selection methods. Here, we use molecular dynamics guided mutagenesis in conjunction with a recently developed microfluidic-based platform, which sorts cells based on their fluorescence photostability, to identify red fluorescent proteins with decreased photobleaching from a HeLa cell-based library. The identified mutant, named Kriek, has 2.5- and 4-fold higher photostability than its progenitor, mCherry, under widefield and confocal illumination, respectively. Furthermore, the results provide insight into mechanisms for enhancing photostability and their connections with other photophysical processes, thereby providing direction for ongoing development of fluorescent proteins with improved single-molecule and low-copy imaging capabilities.
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Affiliation(s)
- Kevin M. Dean
- BioFrontiers Institute, University of Colorado, Boulder, CO, U.S.A
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
| | - Jennifer L. Lubbeck
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
- JILA, NIST, and University of Colorado, Boulder, CO, U.S.A
| | - Lloyd M. Davis
- Center for Laser Applications, University of Tennessee Space Institute, Tullahoma, TN, U.S.A
- Department of Physics, University of Tennessee Knoxville, Knoxville, TN, U.S.A
| | - Chola K. Regmi
- Department of Physics, Florida International University, Miami, FL, U.S.A
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL, U.S.A
| | | | - Ralph Jimenez
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
- JILA, NIST, and University of Colorado, Boulder, CO, U.S.A
| | - Amy E. Palmer
- BioFrontiers Institute, University of Colorado, Boulder, CO, U.S.A
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
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