1
|
Surynt P, Wojtczak BA, Chrominski M, Panecka-Hofman J, Kwapiszewska K, Kalwarczyk T, Kubacka D, Spiewla T, Kasprzyk R, Holyst R, Kowalska J, Jemielity J. Trimethylguanosine cap-fluorescent molecular rotor (TMG-FMR) conjugates are potent, specific snurportin1 ligands enabling visualization in living cells. Org Biomol Chem 2024; 22:6763-6790. [PMID: 39105613 DOI: 10.1039/d4ob01019a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
The trimethylguanosine (TMG) cap is a motif present inter alia at the 5' end of small nuclear RNAs, which are involved in RNA splicing. The TMG cap plays a crucial role in RNA processing and stability as it protects the RNA molecule from degradation by exonucleases and facilitates its export from the nucleus. Additionally, the TMG cap plays a role in the recognition of snRNA by snurportin, a protein that facilitates nuclear import. TMG cap analogs are used in biochemical experiments as molecular tools to substitute the natural TMG cap. To expand the range of available TMG-based tools, here we conjugated the TMG cap to Fluorescent Molecular Rotors (FMRs) to open the possibility of detecting protein-ligand interactions in vitro and, potentially, in vivo, particularly visualizing interactions with snurportin. Consequently, we report the synthesis of 34 differently modified TMG cap-FMR conjugates and their evaluation as molecular probes for snurportin. As FMRs we selected three GFP-like chromophores (derived from green fluorescent protein) and one julolidine derivative. The evaluation of binding affinities for snurportin showed unexpectedly a strong stabilizing effect for TMGpppG-derived dinucleotides containing the FMR at the 2'-O-position of guanosine. These newly discovered compounds are potent snurportin ligands with nanomolar KD (dissociation constant) values, which are two orders of magnitude lower than that of natural TMGpppG. The effect is diminished by ∼50-fold for the corresponding 3'-regioisomers. To deepen the understanding of the structure-activity relationship, we synthesized and tested FMR conjugates lacking the TMG cap moiety. These studies, supported by molecular docking, suggested that the enhanced affinity arises from additional hydrophobic contacts provided by the FMR moiety. The strongest snurportin ligand, which also gave the greatest fluorescence enhancement (Fm/F0) when saturated with the protein, were tested in living cells to detect interactions and visualize complexes by fluorescence lifetime monitoring. This approach has potential applications in the study of RNA processing and RNA-protein interactions.
Collapse
Affiliation(s)
- Piotr Surynt
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Mikolaj Chrominski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Joanna Panecka-Hofman
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Dorota Kubacka
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| |
Collapse
|
2
|
Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
Collapse
Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| |
Collapse
|
3
|
Jimbo M, Otake M, Amano H, Yasumoto K, Watabe S, Okada D, Kumagai H. Characterization of recombinant photoconverting green fluorescent Akanes. J Biochem 2023; 175:25-34. [PMID: 37812399 DOI: 10.1093/jb/mvad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
Akanes are fluorescent proteins that have several fluorescence maxima. In this report, Akane1 and Akane3 from Scleronephthya gracillima were selected, successfully overexpressed in Escherichia coli and purified by affinity chromatography. Fluorescence spectra of the recombinant Akanes matured in darkness, or ambient light were found to have several fluorescence peaks. SDS-PAGE analysis revealed that Akanes matured in ambient light have two fragments. MS/MS analysis of Akanes digested with trypsin showed that the cleavage site is the same as observed for the photoconvertible fluorescent protein Kaede. The differences between the calculated masses from the amino acid sequence of Akane1 and the measured masses of Akane1 fragments obtained under ambient light coincided with those of Kaede. In contrast, a mass difference between the measured N-terminal Akane3 fragment and the calculated mass indicated that Akane3 is modified in the N-terminal region. These results indicate that numerous peaks in the fluorescent spectra of Akanes partly arise from isoproteins of Akanes and photoconversion. Photoconversion of Akane1 caused a fluorescence change from green to red, which was also observed for Akane3; however, the fluorescent intensity decreased dramatically when compared with that of Akane3.
Collapse
Affiliation(s)
- Mitsuru Jimbo
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Mayumi Otake
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Haruna Amano
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Daisuke Okada
- School of Medicine, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Hiroshi Kumagai
- School of Allied Health Sciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| |
Collapse
|
4
|
Barhoum A, Sadak O, Ramirez IA, Iverson N. Stimuli-bioresponsive hydrogels as new generation materials for implantable, wearable, and disposable biosensors for medical diagnostics: Principles, opportunities, and challenges. Adv Colloid Interface Sci 2023; 317:102920. [PMID: 37207377 DOI: 10.1016/j.cis.2023.102920] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023]
Abstract
Hydrogels are excellent water-swollen polymeric materials for use in wearable, implantable, and disposable biosensors. Hydrogels have unique properties such as low cost, ease of preparation, transparency, rapid response to external conditions, biocompatibility and self-adhesion to the skin, flexibility, and strain sensitivity, making them ideal for use in biosensor platforms. This review provides a detailed overview of advanced applications of stimuli-responsive hydrogels in biosensor platforms, from hydrogel synthesis and functionalization for bioreceptor immobilization to several important diagnostic applications. Emphasis is placed on recent advances in the fabrication of ultrasensitive fluorescent and electrically conductive hydrogels and their applications in wearable, implantable, and disposable biosensors for quantitative measurements. Design, modification, and assembly techniques of fluorescent, ionically conductive, and electrically conductive hydrogels to improve performance will be addressed. The advantages and performance improvements of immobilizing bioreceptors (e.g., antibodies, enzymes, and aptamers), and incorporating fluorescent and electrically conductive nanomaterials are described, as are their limitations. Potential applications of hydrogels in implantable, wearable, disposable portable biosensors for quantitative detection of the various bioanalytes (ions, molecules, drugs, proteins, and biomarkers) are discussed. Finally, the global market for hydrogel-based biosensors and future challenges and prospects are discussed in detail.
Collapse
Affiliation(s)
- Ahmed Barhoum
- NanoStruc Research Group, Chemistry Department, Faculty of Science, Helwan University, Cairo 11795, Egypt; National Center for Sensor Research, School of Chemical Sciences, Dublin City University, Dublin 9 D09 Y074, Dublin, Ireland.
| | - Omer Sadak
- Biological Systems Engineering Department, University of Nebraska-Lincoln, Lincoln, NE, USA; Department of Electrical and Electronics Engineering, Ardahan University, Ardahan, Turkey
| | - Ivon Acosta Ramirez
- Biological Systems Engineering Department, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Nicole Iverson
- Biological Systems Engineering Department, University of Nebraska-Lincoln, Lincoln, NE, USA
| |
Collapse
|
5
|
Selection of green fluorescent proteins by in vitro compartmentalization using microbead-display libraries. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
6
|
Vecchia MD, Conte-Daban A, Cappe B, Vandenberg W, Vandenabeele P, Riquet FB, Dedecker P. Spectrally Tunable Förster Resonance Energy Transfer-Based Biosensors Using Organic Dye Grafting. ACS Sens 2022; 7:2920-2927. [PMID: 36162130 DOI: 10.1021/acssensors.2c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Biosensors based on Förster resonance energy transfer (FRET) have revolutionized cellular biology by allowing the direct measurement of biochemical processes in situ. Many genetically encoded sensors make use of fluorescent proteins that are limited in spectral versatility and that allow few ways to change the spectral properties once the construct has been created. In this work, we developed genetically encoded FRET biosensors based on the chemigenetic SNAP and HaloTag domains combined with matching organic fluorophores. We found that the resulting constructs can display comparable responses, kinetics, and reversibility compared to their fluorescent protein-based ancestors, but with the added advantage of spectral versatility, including the availability of red-shifted dye pairs. However, we also find that the introduction of these tags can alter the sensor readout, showing that careful validation is required before applying such constructs in practice. Overall, our approach delivers an innovative methodology that can readily expand the spectral variety and versatility of FRET-based biosensors.
Collapse
Affiliation(s)
- Marco Dalla Vecchia
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium.,Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | | | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Wim Vandenberg
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Peter Dedecker
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| |
Collapse
|
7
|
Bakopoulos D, Whisstock JC, Warr CG, Johnson TK. Macrophage self‐renewal is regulated by transient expression of
PDGF‐ and VEGF‐related factor 2. FEBS J 2022; 289:3735-3751. [DOI: 10.1111/febs.16364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Daniel Bakopoulos
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - James C. Whisstock
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University Clayton Vic. Australia
- Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
| | - Coral G. Warr
- School of Biological Sciences Monash University Clayton Vic. Australia
- School of Molecular Sciences La Trobe University Bundoora Vic. Australia
| | - Travis K. Johnson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University Clayton Vic. Australia
| |
Collapse
|
8
|
Ahmed FH, Caputo AT, French NG, Peat TS, Whitfield J, Warden AC, Newman J, Scott C. Over the rainbow: structural characterization of the chromoproteins gfasPurple, amilCP, spisPink and eforRed. Acta Crystallogr D Struct Biol 2022; 78:599-612. [PMID: 35503208 PMCID: PMC9063845 DOI: 10.1107/s2059798322002625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
Anthozoan chromoproteins are highly pigmented, diversely coloured and readily produced in recombinant expression systems. While they are a versatile and powerful building block in synthetic biology for applications such as biosensor development, they are not widely used in comparison to the related fluorescent proteins, partly due to a lack of structural characterization to aid protein engineering. Here, high-resolution X-ray crystal structures of four open-source chromoproteins, gfasPurple, amilCP, spisPink and eforRed, are presented. These proteins are dimers in solution, and mutation at the conserved dimer interface leads to loss of visible colour development in gfasPurple. The chromophores are trans and noncoplanar in gfasPurple, amilCP and spisPink, while that in eforRed is cis and noncoplanar, and also emits fluorescence. Like other characterized chromoproteins, gfasPurple, amilCP and eforRed contain an sp2-hybridized N-acylimine in the peptide bond preceding the chromophore, while spisPink is unusual and demonstrates a true sp3-hybridized trans-peptide bond at this position. It was found that point mutations at the chromophore-binding site in gfasPurple that substitute similar amino acids to those in amilCP and spisPink generate similar colours. These features and observations have implications for the utility of these chromoproteins in protein engineering and synthetic biology applications.
Collapse
Affiliation(s)
- F. Hafna Ahmed
- Land and Water, CSIRO, Clunies Ross Street, Canberra, ACT 2601, Australia
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia
| | | | - Nigel G. French
- Land and Water, CSIRO, Clunies Ross Street, Canberra, ACT 2601, Australia
| | - Thomas S. Peat
- Manufacturing, CSIRO, Research Way, Clayton, VIC 3168, Australia
| | - Jason Whitfield
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia
- The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Andrew C. Warden
- Land and Water, CSIRO, Clunies Ross Street, Canberra, ACT 2601, Australia
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia
| | - Janet Newman
- Manufacturing, CSIRO, Research Way, Clayton, VIC 3168, Australia
| | - Colin Scott
- Land and Water, CSIRO, Clunies Ross Street, Canberra, ACT 2601, Australia
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT 2601, Australia
| |
Collapse
|
9
|
Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
Collapse
Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
| |
Collapse
|
10
|
Mantovanelli L, Gaastra BF, Poolman B. Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell. CURRENT TOPICS IN MEMBRANES 2021; 88:1-54. [PMID: 34862023 DOI: 10.1016/bs.ctm.2021.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence-based sensors play a fundamental role in biological research. These sensors can be based on fluorescent proteins, fluorescent probes or they can be hybrid systems. The availability of a very large dataset of fluorescent molecules, both genetically encoded and synthetically produced, together with the structural insights on many sensing domains, allowed to rationally design a high variety of sensors, capable of monitoring both molecular and global changes in living cells or in in vitro systems. The advancements in the fluorescence-imaging field helped researchers to obtain a deeper understanding of how and where specific changes occur in a cell or in vitro by combining the readout of the fluorescent sensors with the spatial information provided by fluorescent microscopy techniques. In this review we give an overview of the state of the art in the field of fluorescent biosensors and fluorescence imaging techniques, and eventually guide the reader through the choice of the best combination of fluorescent tools and techniques to answer specific biological questions. We particularly focus on sensors for probing the bioenergetics and physicochemical status of the cell.
Collapse
Affiliation(s)
- Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
11
|
Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV, Sulatskaya AI. New findings on GFP-like protein application as fluorescent tags: Fibrillogenesis, oligomerization, and amorphous aggregation. Int J Biol Macromol 2021; 192:1304-1310. [PMID: 34687761 DOI: 10.1016/j.ijbiomac.2021.10.107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/19/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
Green fluorescent proteins (GFP) are commonly used as fluorescent tags and biosensors in cell biology and medicine. However, the propensity of GFP-like proteins to aggregate and the consequence of intermolecular interaction for their application have not been thoroughly examined. In this work, alternative aggregation pathways of superfolder green fluorescent protein (sfGFP) were demonstrated using a spectroscopic and microscopic study of the samples prepared by equilibrium microdialysis. Besides oligomerization of native monomers, we showed for the first time the condition-specific formation by sfGFP of either amyloid fibrils (at increased temperature or acidity) or amorphous aggregates (at physiological conditions). Both types of sfGFP aggregates had lost green fluorescence and were toxic to cells. Thus, when using GFP-like proteins as fluorescent tags, one should take into account their high ability to form aggregates with lost unique visible fluorescence in the cellular environment, which affects cell viability. Moreover, the results of this work cast doubt on the correctness of the data on the fibrillogenesis of various amyloidogenic proteins obtained using their fusion with GFP-like proteins.
Collapse
Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| |
Collapse
|
12
|
Aarthy M, George A, Ayyadurai N. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review. Int J Biol Macromol 2021; 191:840-851. [PMID: 34560154 DOI: 10.1016/j.ijbiomac.2021.09.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.
Collapse
Affiliation(s)
- Mayilvahanan Aarthy
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Augustine George
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Niraikulam Ayyadurai
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India.
| |
Collapse
|
13
|
Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [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: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
Collapse
Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| |
Collapse
|
14
|
Park S, Nguyen T, Benoit E, Sackett DL, Garmendia-Cedillos M, Pursley R, Boccara C, Gandjbakhche A. Quantitative evaluation of the dynamic activity of HeLa cells in different viability states using dynamic full-field optical coherence microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:6431-6441. [PMID: 34745747 PMCID: PMC8548024 DOI: 10.1364/boe.436330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 05/30/2023]
Abstract
Dynamic full-field optical coherence microscopy (DFFOCM) was used to characterize the intracellular dynamic activities and cytoskeleton of HeLa cells in different viability states. HeLa cell samples were continuously monitored for 24 hours and compared with histological examination to confirm the cell viability states. The averaged mean frequency and magnitude observed in healthy cells were 4.79±0.5 Hz and 2.44±1.06, respectively. In dead cells, the averaged mean frequency was shifted to 8.57±0.71 Hz, whereas the magnitude was significantly decreased to 0.53±0.25. This cell dynamic activity analysis using DFFOCM is expected to replace conventional time-consuming and biopsies-required histological or biochemical methods.
Collapse
Affiliation(s)
- Soongho Park
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Thien Nguyen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Emilie Benoit
- LLTech SAS-Aquyre Biosciences, 58 Rue du Dessous des Berges, 75013 Paris, France
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Marcial Garmendia-Cedillos
- The Signal Processing and Instrumentation Section, Center for Information Technology, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Randall Pursley
- The Signal Processing and Instrumentation Section, Center for Information Technology, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Claude Boccara
- LLTech SAS-Aquyre Biosciences, 58 Rue du Dessous des Berges, 75013 Paris, France
- Institut Langevin, ESPCI Paris, CNRS, PSL University, 1 rue Jussieu, 75005 Paris, France
| | - Amir Gandjbakhche
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| |
Collapse
|
15
|
Anil Sushma A, Zhao B, Tsvetkova IB, Pérez-Segura C, Hadden-Perilla JA, Reilly JP, Dragnea B. Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles. J Phys Chem B 2021; 125:10494-10505. [PMID: 34507491 DOI: 10.1021/acs.jpcb.1c06395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In certain conditions, dye-conjugated icosahedral virus shells exhibit suppression of concentration quenching. The recently observed radiation brightening at high fluorophore densities has been attributed to coherent emission, i.e., to a cooperative process occurring within a subset of the virus-supported fluorophores. Until now, the distribution of fluorophores among potential conjugation sites and the nature of the active subset remained unknown. With the help of mass spectrometry and molecular dynamics simulations, we found which conjugation sites in the brome mosaic virus capsid are accessible to fluorophores. Reactive external surface lysines but also those at the lumenal interface where the coat protein N-termini are located showed virtually unrestricted access to dyes. The third type of labeled lysines was situated at the intercapsomeric interfaces. Through limited proteolysis of flexible N-termini, it was determined that dyes bound to them are unlikely to be involved in the radiation brightening effect. At the same time, specific labeling of genetically inserted cysteines on the exterior capsid surface alone did not lead to radiation brightening. The results suggest that lysines situated within the more rigid structural part of the coat protein provide the chemical environments conducive to radiation brightening, and we discuss some of the characteristics of these environments.
Collapse
Affiliation(s)
- Arathi Anil Sushma
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bingqing Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Irina B Tsvetkova
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
16
|
Sinha RK, Kundu T. Vibronic spectra of jet-cooled 1-methyl-2(1H)-quinolinone studied by Fluorescence spectroscopy and Quantum chemical calculation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118426. [PMID: 32388236 DOI: 10.1016/j.saa.2020.118426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
1-methyl-2(1H)-quinolinone (MeQone) forms the framework of several hundred quinolone alkaloid molecules, both natural and synthetic, which are being used in various biological applications. In this work, we present experimental and theoretical spectroscopic investigation on the MeQone in its ground and first electronic excited states. The vibronically resolved fluorescence excitation (FE) spectrum of MeQone is recorded within 700 cm-1 to the electronic origin under the supersonic jet-cooled condition. The dispersed fluorescence (DF) spectra for bands observed in the FE spectrum were also recorded. Bands observed in DF spectra were identified and assigned with the help of Density Functional Theory (DFT) calculated harmonic vibrational frequencies. Based on the assignments of bands in the ground electronic state and TD-DFT calculated frequencies for the first excited state, we have identified and successfully assigned the bands observed in FE spectrum. This study could be helpful to understand the photophysical properties of MeQone derivatives, the quinolone alkaloids.
Collapse
Affiliation(s)
- Rajeev K Sinha
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
| | - T Kundu
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India.
| |
Collapse
|
17
|
Bridges MC, Woodley CM, Peters EC, May LA, Galloway SB. Expression and Characterization of a Bright Far-red Fluorescent Protein from the Pink-Pigmented Tissues of Porites lobata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:67-80. [PMID: 31853751 DOI: 10.1007/s10126-019-09931-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Members of the anthozoan green fluorescent protein (GFP) family display a diversity of photo-physical properties that can be associated with normal and damaged coral tissues. Poritid coral species often exhibit localized pink pigmentation in diseased or damaged tissues. Our spectral and histological analyses of pink-pigmented Porites lobata lesions show co-localization of bright red fluorescence with putative amoebocytes concentrating in the epidermis, suggesting an activated innate immune response. Here we report the cloning, expression, and characterization of a novel red fluorescent protein (plobRFP) from the pink-pigmented tissues associated with lesions on Porites lobata. In vitro, the recombinant plobRFP exhibits a distinct red emission signal of 614 nm (excitation maximum: 578 nm), making plobRFP the furthest red-shifted natural fluorescent protein isolated from a scleractinian coral. The recombinant protein has a high molar extinction coefficient (84,000 M-1 cm-1) and quantum yield (0.74), conferring a notable brightness to plobRFP. Sequence analysis suggests the distinct brightness and marked red shift may be inherent features of plobRFP's chromophore conformation. While plobRFP displays a tendency to aggregate, its high pH stability, photostability, and spectral properties make it a candidate for cell imaging applications and a potential template for engineering optimized RFPs. The association of plobRFP with a possible immune response furthers its potential use as a visual diagnostic and molecular biomarker for monitoring coral health.
Collapse
Affiliation(s)
- Mary C Bridges
- Graduate Program in Marine Biology, College of Charleston, Charleston, SC, USA
- National Centers for Coastal Ocean Science Charleston Laboratory, NOS, NOAA, Charleston, SC, USA
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Cheryl M Woodley
- National Centers for Coastal Ocean Science Charleston Laboratory, NOS, NOAA, Charleston, SC, USA.
| | - Esther C Peters
- Department of Environmental Science & Policy, George Mason University, Fairfax, VA, USA
| | - Lisa A May
- Consolidated Safety Services, Inc., NCCOS Charleston Laboratory, NOS, NOAA, Charleston, SC, USA
| | - Sylvia B Galloway
- National Centers for Coastal Ocean Science Charleston Laboratory, NOS, NOAA, Charleston, SC, USA
| |
Collapse
|
18
|
Abstract
Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this is far from the truth. Here we shed light on the complexity and importance of diffusion in bacteria, illustrating the similarities and differences of diffusive behaviors of molecules within different compartments of bacterial cells. We first describe common methodologies used to probe diffusion and the associated models and analyses. We then discuss distinct diffusive behaviors of molecules within different bacterial cellular compartments, highlighting the influence of metabolism, size, crowding, charge, binding, and more. We also explicitly discuss where further research and a united understanding of what dictates diffusive behaviors across the different compartments of the cell are required, pointing out new research avenues to pursue.
Collapse
Affiliation(s)
- Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
19
|
Stepanenko OV, Stepanenko OV, Shpironok OG, Fonin AV, Kuznetsova IM, Turoverov KK. Near-Infrared Markers based on Bacterial Phytochromes with Phycocyanobilin as a Chromophore. Int J Mol Sci 2019; 20:ijms20236067. [PMID: 31810174 PMCID: PMC6928796 DOI: 10.3390/ijms20236067] [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: 11/07/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/03/2022] Open
Abstract
Biomarkers engineered on the basis of bacterial phytochromes with biliverdin IXα (BV) cofactor as a chromophore are increasingly used in cell biology and biomedicine, since their absorption and fluorescence spectra lie within the so-called optical “transparency window” of biological tissues. However, the quantum yield of BV fluorescence in these biomarkers does not exceed 0.145. The task of generating biomarkers with a higher fluorescence quantum yield remains relevant. To address the problem, we proposed the use of phycocyanobilin (PCB) as a chromophore of biomarkers derived from bacterial phytochromes. In this work, we characterized the complexes of iRFP713 evolved from RpBphP2 and its mutant variants with different location of cysteine residues capable of covalent tetrapyrrole attachment with the PCB cofactor. All analyzed proteins assembled with PCB were shown to have a higher fluorescence quantum yield than the proteins assembled with BV. The iRFP713/V256C and iRFP713/C15S/V256C assembled with PCB have a particularly high quantum yield of 0.5 and 0.45, which exceeds the quantum yield of all currently available near-infrared biomarkers. Moreover, PCB has 4 times greater affinity for iRFP713/V256C and iRFP713/C15S/V256C proteins compared to BV. These data establish iRFP713/V256C and iRFP713/C15S/V256C assembled with the PCB chromophore as promising biomarkers for application in vivo. The analysis of the spectral properties of the tested biomarkers allowed for suggesting that the high-fluorescence quantum yield of the PCB chromophore can be attributed to the lower mobility of the D-ring of PCB compared to BV.
Collapse
Affiliation(s)
- Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., St. Petersburg 194064, Russia; (O.V.S.); (O.V.S.); (O.G.S.); (A.V.F.); (I.M.K.)
| | - Olga V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., St. Petersburg 194064, Russia; (O.V.S.); (O.V.S.); (O.G.S.); (A.V.F.); (I.M.K.)
| | - Olesya G. Shpironok
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., St. Petersburg 194064, Russia; (O.V.S.); (O.V.S.); (O.G.S.); (A.V.F.); (I.M.K.)
| | - Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., St. Petersburg 194064, Russia; (O.V.S.); (O.V.S.); (O.G.S.); (A.V.F.); (I.M.K.)
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., St. Petersburg 194064, Russia; (O.V.S.); (O.V.S.); (O.G.S.); (A.V.F.); (I.M.K.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., St. Petersburg 194064, Russia; (O.V.S.); (O.V.S.); (O.G.S.); (A.V.F.); (I.M.K.)
- Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya str., 29, St. Petersburg 194064, Russia
- Correspondence: ; Tel.: +7-812-297-19-57
| |
Collapse
|
20
|
A toolkit for expression of Strep-tagged enhanced green fluorescent protein concatemers in mammalian cells. Anal Biochem 2019; 586:113430. [PMID: 31521668 DOI: 10.1016/j.ab.2019.113430] [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: 05/03/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/21/2022]
Abstract
Green fluorescent protein (GFP) and its variants are widely used tools in life sciences. Recently, we and others have used enhanced green fluorescent protein (EGFP) concatemers for determination of nuclear localization signal strength, as natural fluorescence standards and for mapping mobility in living cell nuclei. In this study, we present a molecular toolbox of Strep-tagged EGFP concatemers ranging from 1 to 12 subunits (Addgene plasmids #122488-122499). EGFP concatemers can be easily fused to targeting motifs of any origin by oligonucleotide ligation. Subsequently, we used liposomal transfection for transient expression of EGFP concatemers in eukaryotic cells. We have tested multiple protocols for further processing of the cells and recommend use of formalin or paraformaldehyde/methanol fixation. After usage of these protocols, we were able to detect concatemers by both GFP fluorescence microscopy and αStrep immunomicroscopy. In addition, we observed a more reliable detection of the StrepTag polypeptide (SA-WSHPQFEK) when using αStrepTag antibody instead of StrepTag binding protein. Summing up, we present a toolbox for expression of a wide range of Strep-tagged EGFP concatemers for multiple applications. By use of EGFP fluorescence and/or StrepTag polypeptide, the expressed concatemers can be easily detected in the cell.
Collapse
|
21
|
Tsvetkova IB, Anil Sushma A, Wang JCY, Schaich WL, Dragnea B. Radiation Brightening from Virus-like Particles. ACS NANO 2019; 13:11401-11408. [PMID: 31335115 DOI: 10.1021/acsnano.9b04786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Concentration quenching is a well-known challenge in many fluorescence imaging applications. Here, we show that the optical emission from hundreds of chromophores confined onto the surface of a 28 nm diameter virus particle can be recovered under pulsed irradiation. We have found that as one increases the number of chromophores tightly bound to the virus surface, fluorescence quenching ensues at first, but when the number of chromophores per particle is nearing the maximum number of surface sites allowable, a sudden brightening of the emitted light and a shortening of the excited-state lifetime are observed. This radiation brightening occurs only under short pulse excitation; steady-state excitation is characterized by conventional concentration quenching for any number of chromophores per particle. The observed suppression of fluorescence quenching is consistent with efficient, collective relaxation at room temperature. Interestingly, radiation brightening disappears when the emitters' spatial and/or dynamic heterogeneity is increased, suggesting that the template structural properties may play a role that could be instrumental in developing virus-enabled imaging vectors that have optical properties qualitatively different than those of state-of-the-art biophotonic agents.
Collapse
|
22
|
Singh G, Sridharan D, Khan M, Seshagiri PB. Mouse embryonic stem cell-derived cardiomyocytes cease to beat following exposure to monochromatic light: association with increased ROS and loss of calcium transients. Am J Physiol Cell Physiol 2019; 317:C725-C736. [PMID: 31314584 DOI: 10.1152/ajpcell.00188.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We earlier established the mouse embryonic stem (ES) cell "GS-2" line expressing enhanced green fluorescent protein (EGFP) and have been routinely using it to understand the molecular regulation of differentiation into cardiomyocytes. During such studies, we made a serendipitous discovery that functional cardiomyocytes derived from ES cells stopped beating when exposed to blue light. We observed a gradual cessation of contractility within a few minutes, regardless of wavelength (nm) ranges tested: blue (~420-495), green (~510-575), and red (~600-700), with green light manifesting the strongest impact. Following shifting of cultures back into the incubator (darkness), cardiac clusters regained beatings within a few hours. The observed light-induced contractility-inhibition effect was intrinsic to cardiomyocytes and not due to interference from other cell types. Also, this was not influenced by any physicochemical parameters or intracellular EGFP expression. Interestingly, the light-induced cardiomyocyte contractility inhibition was accompanied by increased intracellular reactive oxygen species (ROS), which could be abolished in the presence of N-acetylcysteine (ROS quencher). Besides, the increased intracardiomyocyte ROS levels were incidental to the inhibition of calcium transients and suppression of mitochondrial activity, both being essential for sarcomere function. To the best of our knowledge, ours is the first report to demonstrate the monochromatic light-mediated inhibition of contractions of cardiomyocytes with no apparent loss of cell viability and contractility. Our findings have implications in cardiac cell biology context in terms of 1) mechanistic insights into light impact on cardiomyocyte contraction, 2) potential use in laser beam-guided (cardiac) microsurgery, photo-optics-dependent medical diagnostics, 3) transient cessation of hearts during coronary artery bypass grafting, and 4) functional preservation of hearts for transplantation.
Collapse
Affiliation(s)
- Gurbind Singh
- Centre for Stem Cell Research, Christian Medical College Campus, Bagayam, Vellore, India
| | - Divya Sridharan
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore, India
| | - Mahmood Khan
- Department of Emergency Medicine, Wexner Medical Centre, Ohio State University, Columbus, Ohio
| | - Polani B Seshagiri
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore, India
| |
Collapse
|
23
|
Tao K, Waletich JR, Wise H, Arredondo F, Tyler BM. Tethering of Multi-Vesicular Bodies and the Tonoplast to the Plasma Membrane in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:636. [PMID: 31396242 PMCID: PMC6662526 DOI: 10.3389/fpls.2019.00636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/26/2019] [Indexed: 05/05/2023]
Abstract
UNLABELLED Tethering of the plasma membrane (PM) and many organelles to the endoplasmic reticulum (ER) for communication and lipid exchange has been widely reported. However, despite growing interest in multi-vesicular bodies (MVBs) as possible sources of exosomes, tethering of MVBs to the PM has not been reported. Here we show that MVBs and the vacuolar membrane (tonoplast) could be tethered to the PM (PM-MVB/TP tethering) by artificial protein fusions or bimolecular fluorescence complementation (BiFC) complexes that contain a peripheral membrane protein that binds the PM and also a protein that binds MVBs or the tonoplast. PM-binding proteins capable of participating in PM-MVB/TP tethering included StRem1.3, BIK1, PBS1, CPK21, and the PtdIns(4)-binding proteins FAPP1 and Osh2. MVB/TP-binding proteins capable of participating in tethering included ARA6, ARA7, RHA1, RABG3f, and the PtdIns(3)P-binding proteins Vam7p and Hrs-2xFYVE. BiFC complexes or protein fusions capable of producing PM-MVB/TP tethering were visualized as large well-defined patches of fluorescence on the PM that could displace PM proteins such as AtFlotillin1 and also could displace cytoplasmic proteins such as soluble GFP. Furthermore, we identified paralogous ubiquitin E3 ligase proteins, SAUL1 (AtPUB44), and AtPUB43 that could produce PM-MVB/TP tethering. SAUL1 and AtPUB43 could produce tethering in uninfected tissue when paired with MVB-binding proteins or when their E3 ligase domain was deleted. When Nicotiana benthamiana leaf tissue was infected with Phytophthora capsici, full length SAUL1 and AtPUB43 localized in membrane patches consistent with PM-MVB/TP tethering. Our findings define new tools for studying PM-MVB/TP tethering and its possible role in plant defense. SIGNIFICANCE STATEMENT Although not previously observed, the tethering of multi-vesicular bodies to the plasma membrane is of interest due to the potential role of this process in producing exosomes in plants. Here we describe tools for observing and manipulating the tethering of multi-vesicular bodies and the tonoplast to the plant plasma membrane, and describe two plant proteins that may naturally regulate this process during infection.
Collapse
Affiliation(s)
- Kai Tao
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin R. Waletich
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Hua Wise
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Felipe Arredondo
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Brett M. Tyler
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, United States
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
- *Correspondence: Brett M. Tyler
| |
Collapse
|
24
|
Kostyuk AI, Panova AS, Bilan DS, Belousov VV. Redox biosensors in a context of multiparameter imaging. Free Radic Biol Med 2018; 128:23-39. [PMID: 29630928 DOI: 10.1016/j.freeradbiomed.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/18/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022]
Abstract
A wide variety of genetically encoded fluorescent biosensors are available to date. Some of them have already contributed significantly to our understanding of biological processes occurring at cellular and organismal levels. Using such an approach, outstanding success has been achieved in the field of redox biology. The probes allowed researchers to observe, for the first time, the dynamics of important redox parameters in vivo during embryogenesis, aging, the inflammatory response, the pathogenesis of various diseases, and many other processes. Given the differences in the readout and spectra of the probes, they can be used in multiparameter imaging in which several processes are monitored simultaneously in the cell. Intracellular processes form an extensive network of interactions. For example, redox changes are often accompanied by changes in many other biochemical reactions related to cellular metabolism and signaling. Therefore, multiparameter imaging can provide important information concerning the temporal and spatial relationship of various signaling and metabolic processes. In this review, we will describe the main types of genetically encoded biosensors, the most frequently used readout, and their use in multiplexed imaging mode.
Collapse
Affiliation(s)
- Alexander I Kostyuk
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anastasiya S Panova
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Institute for Cardiovascular Physiology, Georg August University Göttingen, Göttingen D-37073, Germany.
| |
Collapse
|
25
|
Eroglu E, Charoensin S, Bischof H, Ramadani J, Gottschalk B, Depaoli MR, Waldeck-Weiermair M, Graier WF, Malli R. Genetic biosensors for imaging nitric oxide in single cells. Free Radic Biol Med 2018; 128:50-58. [PMID: 29398285 PMCID: PMC6173299 DOI: 10.1016/j.freeradbiomed.2018.01.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 01/16/2023]
Abstract
UNLABELLED Over the last decades a broad collection of sophisticated fluorescent protein-based probes was engineered with the aim to specifically monitor nitric oxide (NO), one of the most important signaling molecules in biology. Here we report and discuss the characteristics and fields of applications of currently available genetically encoded fluorescent sensors for the detection of NO and its metabolites in different cell types. LONG ABSTRACT Because of its radical nature and short half-life, real-time imaging of NO on the level of single cells is challenging. Herein we review state-of-the-art genetically encoded fluorescent sensors for NO and its byproducts such as peroxynitrite, nitrite and nitrate. Such probes enable the real-time visualization of NO signals directly or indirectly on the level of single cells and cellular organelles and, hence, extend our understanding of the spatiotemporal dynamics of NO formation, diffusion and degradation. Here, we discuss the significance of NO detection in individual cells and on subcellular level with genetic biosensors. Currently available genetically encoded fluorescent probes for NO and nitrogen species are critically discussed in order to provide insights in the functionality and applicability of these promising tools. As an outlook we provide ideas for novel approaches for the design and application of improved NO probes and fluorescence imaging protocols.
Collapse
Affiliation(s)
- Emrah Eroglu
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Suphachai Charoensin
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Helmut Bischof
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Jeta Ramadani
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Benjamin Gottschalk
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Maria R Depaoli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Markus Waldeck-Weiermair
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria; BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria; BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria.
| |
Collapse
|
26
|
Carroll P, Muwanguzi-Karugaba J, Parish T. Codon-optimized DsRed fluorescent protein for use in Mycobacterium tuberculosis. BMC Res Notes 2018; 11:685. [PMID: 30285840 PMCID: PMC6167837 DOI: 10.1186/s13104-018-3798-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE We have previously codon-optimized a number of red fluorescent proteins for use in Mycobacterium tuberculosis (mCherry, tdTomato, Turbo-635). We aimed to expand this repertoire to include DsRed, another widely used and flexible red fluorescent protein. RESULTS We generated expression constructs with a full length DsRed under the control of one of three strong, constitutive promoters (Phsp60, PrpsA or PG13) for use in mycobacteria. We confirmed that full length DsRed (225 amino acids) was expressed and fluoresced brightly. In contrast to mCherry, truncated versions of DsRed lacking several amino acids at the N-terminus were not functional. Thus, we have expanded the repertoire of optimized fluorescent proteins for mycobacteria.
Collapse
Affiliation(s)
- Paul Carroll
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London, UK
| | | | - Tanya Parish
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London, UK
- Infectious Disease Research Institute, Seattle, WA 98102 USA
| |
Collapse
|
27
|
Co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy. Redox Biol 2018; 19:210-217. [PMID: 30176560 PMCID: PMC6120609 DOI: 10.1016/j.redox.2018.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 01/08/2023] Open
Abstract
In order to overcome intercellular variability and thereby effectively assess signal propagation in biological networks it is imperative to simultaneously quantify multiple biological observables in single living cells. While fluorescent biosensors have been the tool of choice to monitor the dynamics of protein interaction and enzymatic activity, co-measuring more than two of them has proven challenging. In this work, we designed three spectrally separated anisotropy-based Förster Resonant Energy Transfer (FRET) biosensors to overcome this difficulty. We demonstrate this principle by monitoring the activation of extrinsic, intrinsic and effector caspases upon apoptotic stimulus. Together with modelling and simulations we show that time of maximum activity for each caspase can be derived from the anisotropy of the corresponding biosensor. Such measurements correlate relative activation times and refine existing models of biological signalling networks, providing valuable insight into signal propagation.
Collapse
|
28
|
Ortega-Villasante C, Burén S, Blázquez-Castro A, Barón-Sola Á, Hernández LE. Fluorescent in vivo imaging of reactive oxygen species and redox potential in plants. Free Radic Biol Med 2018; 122:202-220. [PMID: 29627452 DOI: 10.1016/j.freeradbiomed.2018.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 02/07/2023]
Abstract
Reactive oxygen species (ROS) are by-products of aerobic metabolism, and excessive production can result in oxidative stress and cell damage. In addition, ROS function as cellular messengers, working as redox regulators in a multitude of biological processes. Understanding ROS signalling and stress responses requires methods for precise imaging and quantification to monitor local, subcellular and global ROS dynamics with high selectivity, sensitivity and spatiotemporal resolution. In this review, we summarize the present knowledge for in vivo plant ROS imaging and detection, using both chemical probes and fluorescent protein-based biosensors. Certain characteristics of plant tissues, for example high background autofluorescence in photosynthetic organs and the multitude of endogenous antioxidants, can interfere with ROS and redox potential detection, making imaging extra challenging. Novel methods and techniques to measure in vivo plant ROS and redox changes with better selectivity, accuracy, and spatiotemporal resolution are therefore desirable to fully acknowledge the remarkably complex plant ROS signalling networks.
Collapse
Affiliation(s)
- Cristina Ortega-Villasante
- Fisiología Vegetal, Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Alfonso Blázquez-Castro
- Departamento de Física de Materiales, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Ángel Barón-Sola
- Fisiología Vegetal, Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Luis E Hernández
- Fisiología Vegetal, Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
29
|
Fernández-Luna V, Coto PB, Costa RD. When Fluorescent Proteins Meet White Light-Emitting Diodes. Angew Chem Int Ed Engl 2018; 57:8826-8836. [DOI: 10.1002/anie.201711433] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 12/15/2022]
Affiliation(s)
| | - Pedro B. Coto
- Institut für Theoretische Physik; Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Staudtstr. 7/ B2 91058 Erlangen Germany
- Current address: Department of Physical and Analytical Chemistry; Universidad de Oviedo; Avda. Julián Clavería 8 33006 Oviedo Spain) Department of Physical and Analytical Chemistry
| | - Rubén D. Costa
- IMDEA Materials Institute; C/ Eric Kandel, 2, Tecnogetafe 28906, Getafe Madrid Spain
| |
Collapse
|
30
|
Fernández-Luna V, Coto PB, Costa RD. Wenn fluoreszierende Proteine und Weißlicht emittierende Dioden aufeinandertreffen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - Pedro B. Coto
- Institut für Theoretische Physik; Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Staudtstraße 7/ B2 91058 Erlangen Deutschland
- Aktuelle Adresse: Department of Physical and Analytical Chemistry; Universidad de Oviedo; Avda. Julián Clavería 8 33006 Oviedo Spanien
| | - Rubén D. Costa
- IMDEA Materials Institute; C/ Eric Kandel, 2, Tecnogetafe 28906, Getafe Madrid Spanien
| |
Collapse
|
31
|
Li S, Chen L, Peng X, Wang C, Qin B, Tan D, Han C, Yang H, Ren X, Liu F, Xu C, Zhou X. Overview of the reporter genes and reporter mouse models. Animal Model Exp Med 2018; 1:29-35. [PMID: 30891544 PMCID: PMC6357428 DOI: 10.1002/ame2.12008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/16/2018] [Indexed: 12/31/2022] Open
Abstract
Reporter genes are widely applied in biotechnology and biomedical research owning to their easy observation and lack of toxicity. Taking advantage of the reporter genes in conjunction with imaging technologies, a large number of reporter mouse models have been generated. Reporter mouse models provide systems that enable the studies of live cell imaging, cell lineage tracing, immunological research and cancers etc. in vivo. In this review, we describe the types of different reporter genes and reporter mouse models including, random reporter strains, Cre reporter strains and ROSA26 reporter strains. Collectively, these reporter mouse models have broadened scientific inquires and provided potential strategies for generation of novel reporter animal models with enhanced capabilities.
Collapse
Affiliation(s)
- Shun Li
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Li‐xiang Chen
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Xiu‐hua Peng
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Chao Wang
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Bo‐yin Qin
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Dan Tan
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Cheng‐xiao Han
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hua Yang
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Xiao‐nan Ren
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Fang Liu
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Chun‐hua Xu
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| | - Xiao‐hui Zhou
- Key Laboratory of Medical Molecular VirologyShanghai Public Health Clinical CenterMinistry of Education and HealthFudan UniversityShanghaiChina
| |
Collapse
|
32
|
Stepanenko OV, Stepanenko OV, Bublikov G, Kuznetsova I, Verkhusha V, Turoverov K. Stabilization of structure in near-infrared fluorescent proteins by binding of biliverdin chromophore. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
33
|
A set of enhanced green fluorescent protein concatemers for quantitative determination of nuclear localization signal strength. Anal Biochem 2017; 533:48-55. [PMID: 28669708 DOI: 10.1016/j.ab.2017.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/08/2017] [Accepted: 06/28/2017] [Indexed: 12/17/2022]
Abstract
Regulated transport of proteins between nucleus and cytoplasm is an important process in the eukaryotic cell. In most cases, active nucleo-cytoplasmic protein transport is mediated by nuclear localization signal (NLS) and/or nuclear export signal (NES) motifs. In this study, we developed a set of vectors expressing enhanced GFP (EGFP) concatemers ranging from 2 to 12 subunits (2xEGFP to 12xEGFP) for analysis of NLS strength. As shown by in gel GFP fluorescence analysis and αGFP Western blotting, EGFP concatemers are expressed as fluorescent full-length proteins in eukaryotic cells. As expected, nuclear localization of concatemeric EGFPs decreases with increasing molecular weight. By oligonucleotide ligation this set of EGFP concatemers can be easily fused to NLS motifs. After determination of intracellular localization of EGFP concatemers alone and fused to different NLS motifs we calculated the size of a hypothetic EGFP concatemer showing a defined distribution of EGFP fluorescence between nucleus and cytoplasm (n/c ratio = 2). Clear differences of the size of the hypothetic EGFP concatemer depending on the fused NLS motif were observed. Therefore, we propose to use the size of this hypothetic concatemer as quantitative indicator for comparing strength of different NLS motifs.
Collapse
|
34
|
Pakhomov AA, Chertkova RV, Deyev IE, Petrenko AG, Martynov VI. Generation of photoactivatable fluorescent protein from photoconvertible ancestor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s106816201703013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
35
|
Abstract
Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.
Collapse
Affiliation(s)
- Lynn Sanford
- University of Colorado Boulder, Boulder, CO, United States
| | - Amy Palmer
- University of Colorado Boulder, Boulder, CO, United States.
| |
Collapse
|
36
|
Rougon G, Brasselet S, Debarbieux F. Advances in Intravital Non-Linear Optical Imaging of the Central Nervous System in Rodents. Brain Plast 2016; 2:31-48. [PMID: 29765847 PMCID: PMC5928564 DOI: 10.3233/bpl-160028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose of review: Highly coordinated cellular interactions occur in the healthy or pathologic adult rodent central nervous system (CNS). Until recently, technical challenges have restricted the analysis of these events to largely static modes of study such as immuno-fluorescence and electron microscopy on fixed tissues. The development of intravital imaging with subcellular resolution is required to probe the dynamics of these events in their natural context, the living brain. Recent findings: This review focuses on the recently developed live non-linear optical imaging modalities, the core principles involved, the identified technical challenges that limit their use and the scope of their applications. We highlight some practical applications for these modalities with a specific attention given to Experimental Autoimmune Encephalomyelitis (EAE), a rodent model of a chronic inflammatory disease of the CNS characterized by the formation of disseminated demyelinating lesions accompanied by axonal degeneration. Summary: We conclude that label-free nonlinear optical imaging combined to two photon imaging will continue to contribute richly to comprehend brain function and pathogenesis and to develop effective therapeutic strategies.
Collapse
Affiliation(s)
- Geneviève Rougon
- Aix-Marseille Université, CNRS, Institut des Neurosciences de la Timone, UMR 7289, Marseille, France
| | - Sophie Brasselet
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, Marseille, France
| | - Franck Debarbieux
- Aix-Marseille Université, CNRS, Institut des Neurosciences de la Timone, UMR 7289, Marseille, France
| |
Collapse
|
37
|
Abstract
Myelination by oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system is essential for nervous system function and health. Despite its importance, we have a relatively poor understanding of the molecular and cellular mechanisms that regulate myelination in the living animal, particularly in the CNS. This is partly due to the fact that myelination commences around birth in mammals, by which time the CNS is complex and largely inaccessible, and thus very difficult to image live in its intact form. As a consequence, in recent years much effort has been invested in the use of smaller, simpler, transparent model organisms to investigate mechanisms of myelination in vivo. Although the majority of such studies have employed zebrafish, the Xenopus tadpole also represents an important complementary system with advantages for investigating myelin biology in vivo. Here we review how the natural features of zebrafish embryos and larvae and Xenopus tadpoles make them ideal systems for experimentally interrogating myelination by live imaging. We outline common transgenic technologies used to generate zebrafish and Xenopus that express fluorescent reporters, which can be used to image myelination. We also provide an extensive overview of the imaging modalities most commonly employed to date to image the nervous system in these transparent systems, and also emerging technologies that we anticipate will become widely used in studies of zebrafish and Xenopus myelination in the near future.
Collapse
Affiliation(s)
- Jenea M Bin
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| | - David A Lyons
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
38
|
Roldán-Salgado A, Sánchez-Barreto C, Gaytán P. LanFP10-A, first functional fluorescent protein whose chromophore contains the elusive mutation G67A. Gene 2016; 592:281-90. [PMID: 27418528 DOI: 10.1016/j.gene.2016.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/09/2016] [Indexed: 01/18/2023]
Abstract
Since Green Fluorescent Protein (GFP) was first successfully expressed in heterologous systems in 1994, many genes encoding other natural autofluorescent proteins (AFPs) have been cloned and subsequently modified by protein engineering to improve their physicochemical properties. Throughout this twenty-two-year period, glycine 67 (Gly67) has been regarded as the only amino acid in the entire protein family that is essential for the formation of the different reported chromophores. In this work, we demonstrate that a synthetic gene encoding LanFP10-A, a natural protein encoded in the genome of the lancelet Branchiostoma floridae containing the G67A mutation, produces a heterologous, functional yellow fluorescent protein when expressed in E. coli. In contrast to LanFP10-A, LanFP6-A, a second GFP-like protein found in the lancelet genome that also contains the natural G67A mutation, was non-fluorescent.
Collapse
Affiliation(s)
- Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Celidee Sánchez-Barreto
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico.
| |
Collapse
|
39
|
Roeder E, Matthews BG, Kalajzic I. Visual reporters for study of the osteoblast lineage. Bone 2016; 92:189-195. [PMID: 27616604 PMCID: PMC5056847 DOI: 10.1016/j.bone.2016.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/24/2022]
Abstract
Advancing our understanding of osteoblast biology and differentiation is critical to elucidate the pathological mechanisms responsible for skeletal diseases such as osteoporosis. Histology and histomorphometry, the classical methods to study osteoblast biology, identify osteoblasts based on their location and morphology and ability to mineralize matrix, but do not clearly define their stage of differentiation. Introduction of visual transgenes into the cells of osteoblast lineage has revolutionized the field and resulted in a paradigm shift that allowed for specific identification and isolation of subpopulations within the osteoblast lineage. Knowledge acquired from the studies based on GFP transgenes has allowed for more precise interpretation of studies analyzing targeted overexpression or deletion of genes in the osteoblast lineage. Here, we provide a condensed overview of the currently available promoter-fluorescent reporter transgenic mice that have been generated and evaluated to varying extents. We cover different stages of the lineage as transgenes have been utilized to identify osteoprogenitors, pre-osteoblasts, osteoblasts, or osteocytes. We show that each of these promoters present with advantages and disadvantages. The studies based on the use of these reporter mice have improved our understanding of bone biology. They constitute attractive models to target osteoblasts and help to understand their cell biology.
Collapse
Affiliation(s)
- Emilie Roeder
- Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Brya G Matthews
- Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Ivo Kalajzic
- Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; Department of Pathophysiology, University of Osijek, Osijek, Croatia.
| |
Collapse
|
40
|
Stepanenko OV, Stepanenko OV, Kuznetsova IM, Uversky VN, Turoverov KK. Peculiarities of the Super-Folder GFP Folding in a Crowded Milieu. Int J Mol Sci 2016; 17:ijms17111805. [PMID: 27801849 PMCID: PMC5133806 DOI: 10.3390/ijms17111805] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/11/2016] [Accepted: 10/20/2016] [Indexed: 01/19/2023] Open
Abstract
The natural cellular milieu is crowded by large quantities of various biological macromolecules. This complex environment is characterized by a limited amount of unoccupied space, limited amounts of free water, and changed solvent properties. Obviously, such a tightly packed cellular environment is poorly mimicked by traditional physiological conditions, where low concentrations of a protein of interest are analyzed in slightly salted aqueous solutions. An alternative is given by the use of a model crowded milieu, where a protein of interest is immersed in a solution containing high concentrations of various polymers that serve as model crowding agents. An expected outcome of the presence of such macromolecular crowding agents is their ability to increase conformational stability of a globular protein due to the excluded volume effects. In line with this hypothesis, the behavior of a query protein should be affected by the hydrodynamic size and concentration of an inert crowder (i.e., an agent that does not interact with the protein), whereas the chemical nature of a macromolecular crowder should not play a role in its ability to modulate conformational properties. In this study, the effects of different crowding agents (polyethylene glycols (PEGs) of various molecular masses (PEG-600, PEG-8000, and PEG-12000), Dextran-70, and Ficoll-70) on the spectral properties and unfolding–refolding processes of the super-folder green fluorescent protein (sfGFP) were investigated. sfGFP is differently affected by different crowders, suggesting that, in addition to the expected excluded volume effects, there are some changes in the solvent properties.
Collapse
Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia.
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia.
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia.
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia.
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg State Polytechnic University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia.
| |
Collapse
|
41
|
Buhrke D, Velazquez Escobar F, Sauthof L, Wilkening S, Herder N, Tavraz NN, Willoweit M, Keidel A, Utesch T, Mroginski MA, Schmitt FJ, Hildebrandt P, Friedrich T. The role of local and remote amino acid substitutions for optimizing fluorescence in bacteriophytochromes: A case study on iRFP. Sci Rep 2016; 6:28444. [PMID: 27329837 PMCID: PMC4916461 DOI: 10.1038/srep28444] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/03/2016] [Indexed: 12/30/2022] Open
Abstract
Bacteriophytochromes are promising tools for tissue microscopy and imaging due to their fluorescence in the near-infrared region. These applications require optimization of the originally low fluorescence quantum yields via genetic engineering. Factors that favour fluorescence over other non-radiative excited state decay channels are yet poorly understood. In this work we employed resonance Raman and fluorescence spectroscopy to analyse the consequences of multiple amino acid substitutions on fluorescence of the iRFP713 benchmark protein. Two groups of mutations distinguishing iRFP from its precursor, the PAS-GAF domain of the bacteriophytochrome P2 from Rhodopseudomonas palustris, have qualitatively different effects on the biliverdin cofactor, which exists in a fluorescent (state II) and a non-fluorescent conformer (state I). Substitution of three critical amino acids in the chromophore binding pocket increases the intrinsic fluorescence quantum yield of state II from 1.7 to 5.0% due to slight structural changes of the tetrapyrrole chromophore. Whereas these changes are accompanied by an enrichment of state II from ~40 to ~50%, a major shift to ~88% is achieved by remote amino acid substitutions. Additionally, an increase of the intrinsic fluorescence quantum yield of this conformer by ~34% is achieved. The present results have important implications for future design strategies of biofluorophores.
Collapse
Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Luisa Sauthof
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Svea Wilkening
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Nico Herder
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Neslihan N Tavraz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Mario Willoweit
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Anke Keidel
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Tillmann Utesch
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria-Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Franz-Josef Schmitt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| |
Collapse
|
42
|
Caravagna C, Jaouën A, Debarbieux F, Rougon G. Overview of Innovative Mouse Models for Imaging Neuroinflammation. ACTA ACUST UNITED AC 2016; 6:131-147. [PMID: 27248431 DOI: 10.1002/cpmo.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neuroinflammation demands a comprehensive appraisal in situ to gain in-depth knowledge on the roles of particular cells and molecules and their potential roles in therapy. Because of the lack of appropriate tools, direct visualization of cells has been poorly investigated up to the present. In this context, reporter mice expressing cell-specific fluorescent proteins, combined with multiphoton microscopy, provide a window into cellular processes in living animals. In addition, the ability to collect multiple fluorescent colors from the same sample makes in vivo microscopy uniquely useful for characterizing many parameters from the same area, supporting powerful correlative analyses. Here, we present an overview of the advantages and limitations of this approach, with the purpose of providing insight into the neuroinflammation field. We also provide a review of existing fluorescent mouse models and describe how these models have been used in studies of neuroinflammation. Finally, the potential for developing advanced genetic tools and imaging resources is discussed. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Céline Caravagna
- Aix Marseille Université, CNRS, Institut de Neurosciences de la Timone, Marseille, France.,Aix Marseille Université, Centre Européen de Recherche en Imagerie Médicale, Marseille, France
| | - Alexandre Jaouën
- Aix Marseille Université, CNRS, Institut de Neurosciences de la Timone, Marseille, France.,Aix Marseille Université, Centre Européen de Recherche en Imagerie Médicale, Marseille, France
| | - Franck Debarbieux
- Aix Marseille Université, CNRS, Institut de Neurosciences de la Timone, Marseille, France.,Aix Marseille Université, Centre Européen de Recherche en Imagerie Médicale, Marseille, France.,These authors contributed equally to this work
| | - Geneviève Rougon
- Aix Marseille Université, CNRS, Institut de Neurosciences de la Timone, Marseille, France.,Aix Marseille Université, Centre Européen de Recherche en Imagerie Médicale, Marseille, France.,These authors contributed equally to this work
| |
Collapse
|
43
|
Mattiazzi Usaj M, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol 2016; 26:598-611. [PMID: 27118708 DOI: 10.1016/j.tcb.2016.03.008] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022]
Abstract
High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future.
Collapse
Affiliation(s)
| | - Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Adrian J Verster
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada.
| |
Collapse
|
44
|
Abstract
This chapter describes advantages and limitations of imaging flow cytometry (IFC) based on Imagestream instrumentation using a hybrid approach of morphometric measurement and quantitation of multiparametric fluorescent intensities' distribution in cells and particles. Brief comparison is given of IFC with conventional flow cytometry and fluorescent microscopy. Some future directions of the IFC technology are described and discussed.
Collapse
Affiliation(s)
- Ivan A Vorobjev
- Department of Cell Biology and Histology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Natasha S Barteneva
- Cellular and Molecular Medicine Program, Boston Childrens Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
45
|
Serebrov V, Moore MJ. Single Molecule Approaches in RNA-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:89-106. [DOI: 10.1007/978-3-319-29073-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
46
|
Pakhomov AA, Chertkova RV, Martynov VI. pH-sensor properties of a fluorescent protein from Dendronephthya sp. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:669-74. [DOI: 10.1134/s1068162015060114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
47
|
Shcherbakova K, Nakayama H, Shimamoto N. Role of 100S ribosomes in bacterial decay period. Genes Cells 2015; 20:789-801. [PMID: 26290418 DOI: 10.1111/gtc.12273] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/17/2015] [Indexed: 11/30/2022]
Abstract
Ribosomal proteins S10 and S2 were each fused with GFP to track the fates of these proteins in the stationary growth phase and the following decay period in Escherichia coli. The fused proteins localized mainly in the cytoplasm, and their amounts were proportional to the colony-forming unit. S10-GFP strains that lacked genes responsible for regulating 100S ribosomes and S2-GFP strain that was unable to form 100S both showed shortened stationary phases. This result indicates that these strains exhibit earlier death in the absence of 100S formation (S2-GFP, S10-GFP∆rmf and S10-GFP∆hpf) and breakdown (S10-GFP∆yfiA). Therefore, in addition to the mere presence of 100S, the correct timing of 100S formation and breakdown is required to maintain viability. We propose a model in which 100S acts as a tentative repository of ribosomes that are protected from degradation and provide a source of amino acids in later growth period.
Collapse
Affiliation(s)
- Ksenia Shcherbakova
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, 603-8555, Kyoto, Japan
| | - Hideki Nakayama
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, 603-8555, Kyoto, Japan
| | - Nobuo Shimamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, 603-8555, Kyoto, Japan
| |
Collapse
|
48
|
Close DW, Don Paul C, Langan PS, Wilce MC, Traore DA, Halfmann R, Rocha RC, Waldo GS, Payne RJ, Rucker JB, Prescott M, Bradbury AR. Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering. Proteins 2015; 83:1225-37. [PMID: 25287913 PMCID: PMC4592778 DOI: 10.1002/prot.24699] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/16/2014] [Accepted: 09/27/2014] [Indexed: 01/27/2023]
Abstract
In this article, we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization.
Collapse
Affiliation(s)
- Devin W. Close
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Craig Don Paul
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Patricia S. Langan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Matthew C.J. Wilce
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Daouda A.K. Traore
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Randal Halfmann
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Reginaldo C. Rocha
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Geoffery S. Waldo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | - Mark Prescott
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | |
Collapse
|
49
|
Abstract
FRET (Förster Resonance Energy Transfer) microscopy breaks the resolution limit of light to let us investigate the conformation and function of proteins within living cells. Intensity-based methods are the most popular and direct approach to detect FRET. Among them, detection of sensitized emission signals and ratio imaging of specially designed FRET sensors are routinely used in modern cell biology laboratories. In this chapter, we provide protocols for both these techniques. We guide the reader through the mathematical corrections necessary to calculate the sensitized emission image. We illustrate this approach with an example of studying the interaction of nexin (SNX1) proteins. In the ratio FRET protocol, we focus on monitoring changes in cellular concentration of cAMP with an EPAC-based FRET sensor.
Collapse
|
50
|
Hense A, Nienhaus K, Nienhaus GU. Exploring color tuning strategies in red fluorescent proteins. Photochem Photobiol Sci 2015; 14:200-12. [PMID: 25597270 DOI: 10.1039/c4pp00212a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/31/2014] [Indexed: 01/01/2023]
Abstract
Red-emitting fluorescent proteins (RFPs) with fluorescence emission above 600 nm are advantageous for cell and tissue imaging applications for various reasons. Fluorescence from an RFP is well separated from cellular autofluorescence, which is in the green region of the spectrum, and red light is scattered less, which allows thicker specimens to be imaged. Moreover, the phototoxic response of cells is lower for red than blue or green light exposure. Further red-shifted FP variants can be obtained by genetic modifications causing an extension of the conjugated π-electron system of the chromophore, or by placing amino acids near the chromophore that stabilize its excited state or destabilize its ground state. We have selected the tetrameric RFP eqFP611 from Entacmaea quadricolor as a lead structure and discuss several rational design trials to generate RFP variants with improved photochemical properties.
Collapse
Affiliation(s)
- Anika Hense
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany.
| | | | | |
Collapse
|