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Luan L, Liang D, Chiu DC, Tei R, Baskin JM. Imaging Interorganelle Phospholipid Transport by Extended Synaptotagmins Using Bioorthogonally Tagged Lipids. ACS Chem Biol 2024; 19:1683-1694. [PMID: 39023576 DOI: 10.1021/acschembio.4c00345] [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: 07/20/2024]
Abstract
The proper distribution of lipids within organelle membranes requires rapid interorganelle lipid transport, much of which occurs at membrane contact sites and is mediated by lipid transfer proteins (LTPs). Our current understanding of LTP mechanism and function is based largely on structural studies and in vitro reconstitution. Existing cellular assays for LTP function use indirect readouts, and it remains an open question as to whether substrate specificity and transport kinetics established in vitro are similar in cellular settings. Here, we harness bioorthogonal chemistry to develop tools for direct visualization of interorganelle transport of phospholipids between the plasma membrane (PM) and the endoplasmic reticulum (ER). Unnatural fluorescent phospholipid analogs generated by the transphosphatidylation activity of phospholipase D (PLD) at the PM are rapidly transported to the ER dependent in part upon extended synaptotagmins (E-Syts), a family of LTPs at ER-PM contact sites. Ectopic expression of an artificial E-Syt-based tether at ER-mitochondria contact sites results in fluorescent phospholipid accumulation in mitochondria. Finally, in vitro reconstitution assays demonstrate that the fluorescent lipids are bona fide E-Syt substrates. Thus, fluorescent lipids generated in situ via PLD activity and bioorthogonal chemical tagging can enable direct visualization of the activity of LTPs that mediate bulk phospholipid transport at ER-PM contact sites.
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Affiliation(s)
- Lin Luan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Dongjun Liang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Din-Chi Chiu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Reika Tei
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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2
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Anny CA, Nouaille S, Fauré R, Schulz C, Spriet C, Huvent I, Biot C, Lefebvre T. A Step-by-Step Guide for the Production of Recombinant Fluorescent TAT-HA-Tagged Proteins and their Transduction into Mammalian Cells. Curr Protoc 2024; 4:e1016. [PMID: 38511507 DOI: 10.1002/cpz1.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Investigating the function of target proteins for functional prospection or therapeutic applications typically requires the production and purification of recombinant proteins. The fusion of these proteins with tag peptides and fluorescently derived proteins allows the monitoring of candidate proteins using SDS-PAGE coupled with western blotting and fluorescent microscopy, respectively. However, protein engineering poses a significant challenge for many researchers. In this protocol, we describe step-by-step the engineering of a recombinant protein with various tags: TAT-HA (trans-activator of transduction-hemagglutinin), 6×His and EGFP (enhanced green fluorescent protein) or mCherry. Fusion proteins are produced in E. coli BL21(DE3) cells and purified by immobilized metal affinity chromatography (IMAC) using a Ni-nitrilotriacetic acid (NTA) column. Then, tagged recombinant proteins are introduced into cultured animal cells by using the penetrating peptide TAT-HA. Here, we present a thorough protocol providing a detailed guide encompassing every critical step from plasmid DNA molecular assembly to protein expression and subsequent purification and outlines the conditions necessary for protein transduction technology into animal cells in a comprehensive manner. We believe that this protocol will be a valuable resource for researchers seeking an exhaustive, step-by-step guide for the successful production and purification of recombinant proteins and their entry by transduction within living cells. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA cloning, molecular assembly strategies, and protein production Basic Protocol 2: Protein purification Basic Protocol 3: Protein transduction in mammalian cells.
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Affiliation(s)
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Céline Schulz
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | | | | | - Tony Lefebvre
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
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3
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Chaturvedi M, Patel M, Tiwari A, Dwivedi N, Mondal DP, Srivastava AK, Dhand C. An insight to the recent advancements in detection of Mycobacterium tuberculosis using biosensors: A systematic review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:14-27. [PMID: 38052326 DOI: 10.1016/j.pbiomolbio.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/31/2023] [Accepted: 10/01/2023] [Indexed: 12/07/2023]
Abstract
Since ancient times, Tuberculosis (TB) has been a severe invasive illness that has been prevalent for thousands of years and is also known as "consumption" or phthisis. TB is the most common chronic lung bacterial illness in the world, killing over 2 million people each year, caused by Mycobacterium tuberculosis (MTB). As per the reports of WHO, in spite of technology advancements, the average rate of decline in global TB infections from 2000-2018 was only 1.6% per year, and the worldwide reduction in TB deaths was only 11%. In addition, COVID-19 pandemic has reversed years of global progress in tackling TB with fewer diagnosed cases. The majority of undiagnosed patients of TB are found in low- and middle-income countries where the GeneXpert MTB/RIF assay and sputum smear microscopy have been approved by the WHO as reference procedures for quickly detecting TB. Biosensors, like other cutting-edge technologies, have piqued researchers' interest since they offer a quick and accurate way to identify MTB. Modern integrated technologies allow for the rapid, low-cost, and highly precise detection of analytes in extremely little amounts of sample by biosensors. Here in this review, we outlined the severity of tuberculosis (TB) and the most recent developments in the biosensors sector, as well as their various kinds and benefits for TB detection. The review also emphasizes how widespread TB is and how it needs accurate diagnosis and effective treatment.
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Affiliation(s)
- Mansi Chaturvedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Monika Patel
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Archana Tiwari
- School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Neeraj Dwivedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - D P Mondal
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Avanish Kumar Srivastava
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Chetna Dhand
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Postiglione AE, Adams LL, Ekhator ES, Odelade AE, Patwardhan S, Chaudhari M, Pardue AS, Kumari A, LeFever WA, Tornow OP, Kaoud TS, Neiswinger J, Jeong JS, Parsonage D, Nelson KJ, Kc DB, Furdui CM, Zhu H, Wommack AJ, Dalby KN, Dong M, Poole LB, Keyes JD, Newman RH. Hydrogen peroxide-dependent oxidation of ERK2 within its D-recruitment site alters its substrate selection. iScience 2023; 26:107817. [PMID: 37744034 PMCID: PMC10514464 DOI: 10.1016/j.isci.2023.107817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/11/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are dysregulated in many pervasive diseases. Recently, we discovered that ERK1/2 is oxidized by signal-generated hydrogen peroxide in various cell types. Since the putative sites of oxidation lie within or near ERK1/2's ligand-binding surfaces, we investigated how oxidation of ERK2 regulates interactions with the model substrates Sub-D and Sub-F. These studies revealed that ERK2 undergoes sulfenylation at C159 on its D-recruitment site surface and that this modification modulates ERK2 activity differentially between substrates. Integrated biochemical, computational, and mutational analyses suggest a plausible mechanism for peroxide-dependent changes in ERK2-substrate interactions. Interestingly, oxidation decreased ERK2's affinity for some D-site ligands while increasing its affinity for others. Finally, oxidation by signal-generated peroxide enhanced ERK1/2's ability to phosphorylate ribosomal S6 kinase A1 (RSK1) in HeLa cells. Together, these studies lay the foundation for examining crosstalk between redox- and phosphorylation-dependent signaling at the level of kinase-substrate selection.
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Affiliation(s)
- Anthony E. Postiglione
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Laquaundra L. Adams
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Ese S. Ekhator
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anuoluwapo E. Odelade
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Supriya Patwardhan
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Meenal Chaudhari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Computational Data Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Mathematics and Computer Science, University of Virginia at Wise, Wise, VA 24293, USA
| | - Avery S. Pardue
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anjali Kumari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - William A. LeFever
- Department of Chemistry, High Point University, High Point, NC 27268, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Olivia P. Tornow
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Tamer S. Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Johnathan Neiswinger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Belhaven University, Jackson, MS 39202, USA
| | - Jun Seop Jeong
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J. Nelson
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Dukka B. Kc
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew J. Wommack
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming Dong
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jeremiah D. Keyes
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Biology, Penn State University Behrend, Erie, PA 16563, USA
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Robert H. Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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Zeghal M, Matte K, Venes A, Patel S, Laroche G, Sarvan S, Joshi M, Rain JC, Couture JF, Giguère PM. Development of a V5-tag-directed nanobody and its implementation as an intracellular biosensor of GPCR signaling. J Biol Chem 2023; 299:105107. [PMID: 37517699 PMCID: PMC10470007 DOI: 10.1016/j.jbc.2023.105107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
Protein-protein interactions (PPIs) form the foundation of any cell signaling network. Considering that PPIs are highly dynamic processes, cellular assays are often essential for their study because they closely mimic the biological complexities of cellular environments. However, incongruity may be observed across different PPI assays when investigating a protein partner of interest; these discrepancies can be partially attributed to the fusion of different large functional moieties, such as fluorescent proteins or enzymes, which can yield disparate perturbations to the protein's stability, subcellular localization, and interaction partners depending on the given cellular assay. Owing to their smaller size, epitope tags may exhibit a diminished susceptibility to instigate such perturbations. However, while they have been widely used for detecting or manipulating proteins in vitro, epitope tags lack the in vivo traceability and functionality needed for intracellular biosensors. Herein, we develop NbV5, an intracellular nanobody binding the V5-tag, which is suitable for use in cellular assays commonly used to study PPIs such as BRET, NanoBiT, and Tango. The NbV5:V5 tag system has been applied to interrogate G protein-coupled receptor signaling, specifically by replacing larger functional moieties attached to the protein interactors, such as fluorescent or luminescent proteins (∼30 kDa), by the significantly smaller V5-tag peptide (1.4 kDa), and for microscopy imaging which is successfully detected by NbV5-based biosensors. Therefore, the NbV5:V5 tag system presents itself as a versatile tool for live-cell imaging and a befitting adaptation to existing cellular assays dedicated to probing PPIs.
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Affiliation(s)
- Manel Zeghal
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kevin Matte
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Angelica Venes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Shivani Patel
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Sabina Sarvan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Monika Joshi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrick M Giguère
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
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6
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Li J, Liu B, Liu L, Zhang N, Liao Y, Zhao C, Cao M, Zhong Y, Chai D, Chen X, Zhang D, Wang H, He Y, Li Z. Fluorescence-based aptasensors for small molecular food contaminants: From energy transfer to optical polarization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121872. [PMID: 36152504 DOI: 10.1016/j.saa.2022.121872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Small molecular food contaminants, such as mycotoxins, pesticide residues and antibiotics, are highly probable to be passively introduced in food at all stages of its processing, including planting, harvest, production, transportation and storage. Owing to the high risks caused by the unknowing intake and accumulation in human, there is an urgent need to develop rapid, sensitive and efficient methods to monitor them. Fluorescence-based aptasensors provide a promising platform for this area owing to its simple operation, high sensitivity, wide application range and economical practicability. In this paper, the common sorts of small molecular contaminants in foods, namely mycotoxins, pesticides, antibiotics, etc, are briefly introduced. Then, we make a comprehensive review, from fluorescence resonance energy transfer (in turn-on, turn-off, and ratiometric mode, as well as energy upconversion) to fluorescence polarization, of the fluorescence-based aptasensors for the determination of these food contaminants reported in the last five years. The principle of signal generation, the advances of each sort of fluorescent aptasensors, as well as their applications are introduced in detail. Additionally, we also discussed the challenges and perspectives of the fluorescent aptasensors for small molecular food contaminants. This work will offer systematic overview and inspiration for amateurs, researchers and developers of fluorescence-based aptasensors for the detection of small molecules.
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Affiliation(s)
- Jingrong Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Boshi Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Li Liu
- Library of Tianjin Medical University, Tianjin 300070, China
| | - Nan Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yumeng Liao
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chunyu Zhao
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Manzhu Cao
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuxuan Zhong
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Danni Chai
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoyu Chen
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Di Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Haixia Wang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Yongzhi He
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
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7
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Van Thillo T, Van Deuren V, Dedecker P. Smart genetically-encoded biosensors for the chemical monitoring of living systems. Chem Commun (Camb) 2023; 59:520-534. [PMID: 36519509 DOI: 10.1039/d2cc05363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetically-encoded biosensors provide the all-optical and non-invasive visualization of dynamic biochemical events within living systems, which has allowed the discovery of profound new insights. Twenty-five years of biosensor development has steadily improved their performance and has provided us with an ever increasing biosensor repertoire. In this feature article, we present recent advances made in biosensor development and provide a perspective on the future direction of the field.
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Affiliation(s)
- Toon Van Thillo
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Vincent Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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8
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Mizutani Y, Mizuno M. Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale. J Chem Phys 2022; 157:240901. [PMID: 36586981 DOI: 10.1063/5.0116734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.
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Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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9
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Deng H, Chen Y, Xu L, Mo X, Ju J, Yu C, Zhu X. A Biomimetic Emitter Inspired from Green Fluorescent Protein. J Phys Chem B 2022; 126:8771-8776. [PMID: 36278933 DOI: 10.1021/acs.jpcb.2c07131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The unique tripeptide structure of green fluorescent protein (GFP), a Ser-Tyr-Gly motif, generates the mature chromophore in situ to define the emission profiles of GFP. Here, we describe the rational design and discovery of a biomimetic fluorescent emitter, MBP, by mimicking the key structure of the Ser-Tyr-Gly motif. Through systematically tailoring the tripeptide, a family of four chromophores were engineered, while only MBP exhibited bright fluorescence in different fluid solvents with highly enhanced quantum yields. Distinct to previous hydrogen-bonding-induced fluorescence quenching of GFP chromophore analogues, the emission of MBP was only slightly decreased in protic solvents. Heteronuclear multiple bond correlation techniques demonstrated the fundamental mechanism for enhanced fluorescence emission owing to the synergy of the formation of the intramolecular hydrogen-bonding-ring structure and the self-restricted effect, which was further illustrated via theoretical calculations. This work puts forward an extraordinary approach toward highly emissive biomimicking fluorophores, which gives new insights into the emission mechanisms and photophysics of GFP-like chromophores.
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Affiliation(s)
- Hongping Deng
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Yan Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, China
| | - Li Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Xuan Mo
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Jingxuan Ju
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Chunyang Yu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, China
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10
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Li J, Zhang L, Chen J, Zhang R, Liu Z, Zhao J, Liu B, Han MY, Han G, Zhang Z. One-step synthesized amphiphilic carbon dots for the super-resolution imaging of endoplasmic reticulum in live cells. RSC Adv 2022; 12:19424-19430. [PMID: 35865591 PMCID: PMC9255560 DOI: 10.1039/d2ra02705d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022] Open
Abstract
Stimulated emission depletion (STED) microscopy provides a powerful tool for visualizing the ultrastructure and dynamics of subcellular organelles, however, the photobleaching of organelle trackers have limited the application of STED imaging in living cells. Here, we report photostable and amphiphilic carbon dots (Phe-CDs) with bright orange fluorescence via a simple one-pot hydrothermal treatment of o-phenylenediamine and phenylalanine. The obtained Phe-CDs not only had high brightness (quantum yield ∼18%) but also showed excellent photostability under ultraviolet irradiation. The CDs can quickly penetrate into cells within 2 min and are specific for intracellular ER. The further investigations by Phe-CDs revealed the reconstitution process of ER from loosely spaced tubes into a continuously dense network of tubules and sheets during cell division. Importantly, compared with the standard microscopy, STED super-resolution imaging allowed the tracking of the ER ultrastructure with a lateral resolution less than 100 nm and the pores within the ER network are clearly visible. Moreover, the three dimensional (3D) structure of ER was also successfully reconstructed from z-stack images due to the excellent photostability of Phe-CDs. Amphiphilic carbon dots (Phe-CDs) were synthesized directly via one-step hydrothermal reaction for specific ER targeting without further modification. The Phe-CDs were photostable enough to allow STED super-resolution imaging of ER in live cells.![]()
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Affiliation(s)
- Jiajia Li
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Longdi Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Juan Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Ruilong Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Zhengjie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Jun Zhao
- Key Lab of Photovoltaic and Energy Conservation Materials, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences Hefei 230031 P. R. China
| | - Bianhua Liu
- Key Lab of Photovoltaic and Energy Conservation Materials, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences Hefei 230031 P. R. China
| | - Ming-Yong Han
- Key Lab of Photovoltaic and Energy Conservation Materials, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences Hefei 230031 P. R. China
| | - Guangmei Han
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Zhongping Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Chemistry and Chemical Engineering, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China .,Key Lab of Photovoltaic and Energy Conservation Materials, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences Hefei 230031 P. R. China
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11
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Yang JM, Chi WY, Liang J, Takayanagi S, Iglesias PA, Huang CH. Deciphering cell signaling networks with massively multiplexed biosensor barcoding. Cell 2021; 184:6193-6206.e14. [PMID: 34838160 PMCID: PMC8686192 DOI: 10.1016/j.cell.2021.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.
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Affiliation(s)
- Jr-Ming Yang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
| | - Wei-Yu Chi
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jessica Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Saki Takayanagi
- XDBio Graduate Program, Johns Hopkins School of Medicine, MD 21205, USA
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chuan-Hsiang Huang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
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12
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Zhang J, Li H, Lin B, Luo X, Yin P, Yi T, Xue B, Zhang XL, Zhu H, Nie Z. Development of Near-Infrared Nucleic Acid Mimics of Fluorescent Proteins for In Vivo Imaging of Viral RNA with Turn-On Fluorescence. J Am Chem Soc 2021; 143:19317-19329. [PMID: 34762804 DOI: 10.1021/jacs.1c04577] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
GFP-like fluorescent proteins and their molecular mimics have revolutionized bioimaging research, but their emissions are largely limited in the visible to far-red region, hampering the in vivo applications in intact animals. Herein, we structurally modulate GFP-like chromophores using a donor-acceptor-acceptor (D-A-A') molecular configuration to discover a set of novel fluorogenic derivatives with infrared-shifted spectra. These chromophores can be fluorescently elicited by their specific interaction with G-quadruplex (G4), a unique noncanonical nucleic acid secondary structure, via inhibition of the chromophores' twisted-intramolecular charge transfer. This feature allows us to create, for the first time, FP mimics with tunable emission in the near-infrared (NIR) region (Emmax = 664-705 nm), namely, infrared G-quadruplex mimics of FPs (igMFP). Compared with their FP counterparts, igMFPs exhibit remarkably higher quantum yields, larger Stokes shift, and better photostability. In a proof-of-concept application using pathogen-related G4s as the target, we exploited igMFPs to directly visualize native hepatitis C virus (HCV) RNA genome in living cells via their in situ formation by the chromophore-bound viral G4 structure in the HCV core gene. Furthermore, igMFPs are capable of high contrast HCV RNA imaging in living mice bearing a HCV RNA-presenting mini-organ, providing the first application of FP mimics in whole-animal imaging.
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Affiliation(s)
- Jiaheng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Peng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Ting Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Binbin Xue
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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13
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Sharath Kumar KS, Girish YR, Ashrafizadeh M, Mirzaei S, Rakesh KP, Hossein Gholami M, Zabolian A, Hushmandi K, Orive G, Kadumudi FB, Dolatshahi-Pirouz A, Thakur VK, Zarrabi A, Makvandi P, Rangappa KS. AIE-featured tetraphenylethylene nanoarchitectures in biomedical application: Bioimaging, drug delivery and disease treatment. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214135] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Boulanger SA, Chen C, Myasnyanko IN, Sokolov AI, Baranov MS, Fang C. Excited-State Dynamics of a meta-Dimethylamino Locked GFP Chromophore as a Fluorescence Turn-on Water Sensor †. Photochem Photobiol 2021; 98:311-324. [PMID: 34714942 DOI: 10.1111/php.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022]
Abstract
Strategic incorporation of a meta-dimethylamino (-NMe2 ) group on the conformationally locked green fluorescent protein (GFP) model chromophore (m-NMe2 -LpHBDI) has drastically altered molecular electronic properties, counterintuitively enhancing fluorescence of only the neutral and cationic chromophores in aqueous solution. A ˜200-fold decrease in fluorescence quantum yield of m-NMe2 -LpHBDI in alcohols (e.g., MeOH, EtOH and 2-PrOH) supports this GFP-derived compound as a fluorescence turn-on water sensor, with large fluorescence intensity differences between H2 O and ROH emissions in various H2 O/ROH binary mixtures. A combination of steady-state electronic spectroscopy, femtosecond transient absorption, ground-state femtosecond stimulated Raman spectroscopy (FSRS) and quantum calculations elucidates an intermolecular hydrogen-bonding chain between a solvent -OH group and the chromophore phenolic ring -NMe2 and -OH functional groups, wherein fluorescence differences arise from an extended hydrogen-bonding network beyond the first solvation shell, as opposed to fluorescence quenching via a dark twisted intramolecular charge-transfer state. The absence of a meta-NMe2 group twisting coordinate upon electronic excitation was corroborated by experiments on control samples without the meta-NMe2 group or with both meta-NMe2 and para-OH groups locked in a six-membered ring. These deep mechanistic insights stemming from GFP chromophore scaffold will enable rational design of organic, compact and environmentally friendly water sensors.
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Affiliation(s)
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, OR
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, OR
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15
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Khrenova MG, Mulashkin FD, Nemukhin AV. Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation. J Chem Inf Model 2021; 61:5125-5132. [PMID: 34601882 DOI: 10.1021/acs.jcim.1c00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a model for spectral tuning in red fluorescent proteins (RFPs) based on the relation between an electronic structure descriptor, the dipole moment variation upon excitation (DMV), and the excitation energy of a protein. This approach aims to overcome the problem of accurate prediction of excitation energies in RFPs, which span a very narrow window of band maxima. The latter roughly corresponds to the energy range of 0.1 eV, which is comparable with typical errors in calculations of the excitation energy by conventional quantum chemistry methods. In this work, we demonstrate a strong quantitative correlation between DMV values, obtained computationally with modest efforts, and excitation energies ΔEex at the experimental excitation band maxima for a series of RFPs with bands between 570 and 605 nm. Protein models are constructed by motifs of the relevant crystal structures, and atomic coordinates are optimized in quantum mechanics/molecular mechanics (QM/MM) calculations with QM-subsystems composed of large chromophore-containing regions. DMV values are evaluated with the electron density computed at the time-dependent density functional theory (TDDFT) level using several functionals and basis sets. We show that the results obtained with the CAM-B3LYP, BHHLYP, and M06-2X functionals demonstrate favorable correlations between DMV and ΔEex with the mean absolute error less than 0.01 eV. Taking into account the solid theoretical grounds of the relation between the DMV and the excitation energy in fluorescent proteins, the described modeling strategy presents a rational tool for spectral tuning in these efficient markers for in vivo imaging.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Fedor D Mulashkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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16
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Zhang L, Takahashi Y, Schroeder JI. Protein kinase sensors: an overview of new designs for visualizing kinase dynamics in single plant cells. PLANT PHYSIOLOGY 2021; 187:527-536. [PMID: 35142856 PMCID: PMC8491035 DOI: 10.1093/plphys/kiab277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/16/2021] [Indexed: 05/15/2023]
Abstract
Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor's working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO2 merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.
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Affiliation(s)
- Li Zhang
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, California 92093, USA
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Yohei Takahashi
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, California 92093, USA
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17
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In situ observation of mitochondrial biogenesis as the early event of apoptosis. iScience 2021; 24:103038. [PMID: 34553131 PMCID: PMC8441175 DOI: 10.1016/j.isci.2021.103038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/28/2021] [Accepted: 08/22/2021] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial biogenesis is a cell response to external stimuli which is generally believed to suppress apoptosis. However, during the process of apoptosis, whether mitochondrial biogenesis occurs in the early stage of the apoptotic cells remains unclear. To address this question, we constructed the COX8-EGFP-ACTIN-mCherry HeLa cells with recombinant fluorescent proteins respectively tagged on the nucleus and mitochondria and monitored the mitochondrial changes in the living cells exposed to gamma-ray radiation. Besides in situ detection of mitochondrial fluorescence changes, we also examined the cell viability, nuclear DNA damage, reactive oxygen species (ROS), mitochondrial superoxide, citrate synthase activity, ATP, cytoplasmic and mitochondrial calcium, mitochondrial mass, mitochondrial morphology, and protein expression related to mitochondrial biogenesis, as well as the apoptosis biomarkers. As a result, we confirmed that significant mitochondrial biogenesis took place preceding the radiation-induced apoptosis, and it was closely correlated with the apoptotic cells at late stage. The involved mechanism was also discussed. Dual fluorescence approach was used for in situ observation of living cell processes Radiation-induced effects of mitochondrial biogenesis and apoptosis were observed Relationship between mitochondrial biogenesis and apoptosis was revisited Assessing early mitochondrial biogenesis is critical for predicting later fate of cells
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18
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Wolf S, Wan Y, McDole K. Current approaches to fate mapping and lineage tracing using image data. Development 2021; 148:dev198994. [PMID: 34498046 DOI: 10.1242/dev.198994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visualizing, tracking and reconstructing cell lineages in developing embryos has been an ongoing effort for well over a century. Recent advances in light microscopy, labelling strategies and computational methods to analyse complex image datasets have enabled detailed investigations into the fates of cells. Combined with powerful new advances in genomics and single-cell transcriptomics, the field of developmental biology is able to describe the formation of the embryo like never before. In this Review, we discuss some of the different strategies and applications to lineage tracing in live-imaging data and outline software methodologies that can be applied to various cell-tracking challenges.
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Affiliation(s)
- Steffen Wolf
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yinan Wan
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Katie McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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19
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Secilmis M, Altun HY, Pilic J, Erdogan YC, Cokluk Z, Ata BN, Sevimli G, Zaki AG, Yigit EN, Öztürk G, Malli R, Eroglu E. A Co-Culture-Based Multiparametric Imaging Technique to Dissect Local H 2O 2 Signals with Targeted HyPer7. BIOSENSORS 2021; 11:338. [PMID: 34562927 PMCID: PMC8466187 DOI: 10.3390/bios11090338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/19/2023]
Abstract
Multispectral live-cell imaging is an informative approach that permits detecting biological processes simultaneously in the spatial and temporal domain by exploiting spectrally distinct biosensors. However, the combination of fluorescent biosensors with distinct spectral properties such as different sensitivities, and dynamic ranges can undermine accurate co-imaging of the same analyte in different subcellular locales. We advanced a single-color multiparametric imaging method, which allows simultaneous detection of hydrogen peroxide (H2O2) in multiple cell locales (nucleus, cytosol, mitochondria) using the H2O2 biosensor HyPer7. Co-culturing of endothelial cells stably expressing differentially targeted HyPer7 biosensors paved the way for co-imaging compartmentalized H2O2 signals simultaneously in neighboring cells in a single experimental setup. We termed this approach COMPARE IT, which is an acronym for co-culture-based multiparametric imaging technique. Employing this approach, we detected lower H2O2 levels in mitochondria of endothelial cells compared to the cell nucleus and cytosol under basal conditions. Upon administering exogenous H2O2, the cytosolic and nuclear-targeted probes displayed similarly slow and moderate HyPer7 responses, whereas the mitochondria-targeted HyPer7 signal plateaued faster and reached higher amplitudes. Our results indicate striking differences in mitochondrial H2O2 accumulation of endothelial cells. Here, we present the method's potential as a practicable and informative multiparametric live-cell imaging technique.
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Affiliation(s)
- Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Hamza Yusuf Altun
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Johannes Pilic
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Yusuf Ceyhun Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Busra Nur Ata
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Esra Nur Yigit
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Department of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Physiology Department, International School of Medicine, Istanbul Medipol University, 34810 Istanbul, Turkey
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Nanotechnology Research and Application Center, Sabanci University, 34956 Istanbul, Turkey
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20
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Floerchinger A, Murphy KJ, Latham SL, Warren SC, McCulloch AT, Lee YK, Stoehr J, Mélénec P, Guaman CS, Metcalf XL, Lee V, Zaratzian A, Da Silva A, Tayao M, Rolo S, Phimmachanh M, Sultani G, McDonald L, Mason SM, Ferrari N, Ooms LM, Johnsson AKE, Spence HJ, Olson MF, Machesky LM, Sansom OJ, Morton JP, Mitchell CA, Samuel MS, Croucher DR, Welch HCE, Blyth K, Caldon CE, Herrmann D, Anderson KI, Timpson P, Nobis M. Optimizing metastatic-cascade-dependent Rac1 targeting in breast cancer: Guidance using optical window intravital FRET imaging. Cell Rep 2021; 36:109689. [PMID: 34525350 DOI: 10.1016/j.celrep.2021.109689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 07/06/2021] [Accepted: 08/18/2021] [Indexed: 01/18/2023] Open
Abstract
Assessing drug response within live native tissue provides increased fidelity with regards to optimizing efficacy while minimizing off-target effects. Here, using longitudinal intravital imaging of a Rac1-Förster resonance energy transfer (FRET) biosensor mouse coupled with in vivo photoswitching to track intratumoral movement, we help guide treatment scheduling in a live breast cancer setting to impair metastatic progression. We uncover altered Rac1 activity at the center versus invasive border of tumors and demonstrate enhanced Rac1 activity of cells in close proximity to live tumor vasculature using optical window imaging. We further reveal that Rac1 inhibition can enhance tumor cell vulnerability to fluid-flow-induced shear stress and therefore improves overall anti-metastatic response to therapy during transit to secondary sites such as the lung. Collectively, this study demonstrates the utility of single-cell intravital imaging in vivo to demonstrate that Rac1 inhibition can reduce tumor progression and metastases in an autochthonous setting to improve overall survival.
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Affiliation(s)
- Alessia Floerchinger
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kendelle J Murphy
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sharissa L Latham
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sean C Warren
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Andrew T McCulloch
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Young-Kyung Lee
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Janett Stoehr
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Pauline Mélénec
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Cris S Guaman
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Xanthe L Metcalf
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Victoria Lee
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Andrew Da Silva
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael Tayao
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sonia Rolo
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Monica Phimmachanh
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Ghazal Sultani
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Laura McDonald
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Susan M Mason
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Nicola Ferrari
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Lisa M Ooms
- Cancer Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | | | - Heather J Spence
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael F Olson
- Department of Chemistry and Biology, Ryerson University, Toronto ON, M5B 2K3, Canada
| | - Laura M Machesky
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Jennifer P Morton
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Michael S Samuel
- Centre for Cancer Biology, SA Pathology and University of South Australia; and the School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - David R Croucher
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Heidi C E Welch
- Signalling Programme, Babraham Institute, Cambridge CB223AT, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - C Elizabeth Caldon
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - David Herrmann
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kurt I Anderson
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Francis Crick Institute, London NW11AT, UK
| | - Paul Timpson
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia.
| | - Max Nobis
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia.
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21
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Stellon D, Tran MTN, Talbot J, Chear S, Khalid MKNM, Pébay A, Vickers JC, King AE, Hewitt AW, Cook AL. CRISPR/Cas-Mediated Knock-in of Genetically Encoded Fluorescent Biosensors into the AAVS1 Locus of Human-Induced Pluripotent Stem Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2549:379-398. [PMID: 34505269 DOI: 10.1007/7651_2021_422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded fluorescent biosensors (GEFBs) enable researchers to visualize and quantify cellular processes in live cells. Induced pluripotent stem cells (iPSCs) can be genetically engineered to express GEFBs via integration into the Adeno-Associated Virus Integration Site 1 (AAVS1) safe harbor locus. This can be achieved using CRISPR/Cas ribonucleoprotein targeting to cause a double-strand break at the AAVS1 locus, which subsequently undergoes homology-directed repair (HDR) in the presence of a donor plasmid containing the GEFB sequence. We describe an optimized protocol for CRISPR/Cas-mediated knock-in of GEFBs into the AAVS1 locus of human iPSCs that allows puromycin selection and which exhibits negligible off-target editing. The resulting iPSC lines can be differentiated into cells of different lineages while retaining expression of the GEFB, enabling live-cell interrogation of cell pathway activities across a diversity of disease models.
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Affiliation(s)
- David Stellon
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia.
| | | | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | | | - Alice Pébay
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia.,Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia.
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22
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Multicolor 3D Confocal Imaging of Thick Tissue Sections. Methods Mol Biol 2021; 2350:95-104. [PMID: 34331281 DOI: 10.1007/978-1-0716-1593-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
In multicellular organisms, most physiological and pathological processes involve an interplay between various cells and molecules that act both locally and systemically. To understand how these complex and dynamic processes occur in time and space, imaging techniques are key. Advances in tissue processing techniques and microscopy now allow us to probe these processes at a large scale and at the same time at a level of detail previously unachievable. Indeed, it is now possible to reliably quantify multiple protein expression levels at single-cell resolution in whole organs using three-dimensional fluorescence imaging techniques. Here we describe a method to prepare adult mouse bone tissue for multiplexed confocal imaging of thick tissue sections. Up to eight different fluorophores can be multiplexed using this technique and spectrally resolved using standard confocal microscopy. The optical clearing method described allows detection of these fluorophores up to a depth of >700 μm in the far-red. Although the method was initially developed for bone tissue imaging, we have successfully applied it to several other tissue types.
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23
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Zheng Y, Wei L, Duan L, Yang F, Huang G, Xiao T, Wei M, Liang Y, Yang H, Li Z, Wang D. Rapid field testing of mercury pollution by designed fluorescent biosensor and its cells-alginate hydrogel-based paper assay. J Environ Sci (China) 2021; 106:161-170. [PMID: 34210432 DOI: 10.1016/j.jes.2021.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 06/13/2023]
Abstract
With increasing industrial activities, mercury has been largely discharged into environment and caused serious environmental problems. The growing level of mercury pollution has become a huge threat to human health due to its significant biotoxicity. Therefore, the simple and fast means for on-site monitoring discharged mercury pollution are highly necessary to protect human beings from its pernicious effects in time. Herein, a "turn off" fluorescent biosensor (mCherry L199C) for sensing Hg2+ was successfully designed based on direct modification of the chromophore environment of fluorescent protein mCherry. For rapid screening and characterization, the designed variant of mCherry (mCherry L199C) was directly expressed on outer-membrane of Escherichia coli cells by cell surface display technique. The fluorescent biosensor was characterized to have favorable response to Hg2+ at micromole level among other metal ions and over a broad pH range. Further, the cells of the fluorescent biosensor were encapsulated in alginate hydrogel to develop the cells-alginate hydrogel-based paper. The cells-alginate hydrogel-based paper could detect mercury pollution in 5 min with simple operation process and inexpensive equipment, and it could keep fluorescence and activity stable at 4 °C for 24 hr, which would be a high-throughput screening tool in preliminarily reporting the presence of mercury pollution in natural setting.
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Affiliation(s)
- Yanan Zheng
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Liudan Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Linwei Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‑Bioresources, Guangxi University, Nanning 530004, China
| | - Fangfang Yang
- Guangxi-ASEAN Food Inspection and Testing Center, China
| | - Guixiang Huang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Tianyi Xiao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Min Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Yanling Liang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Huiting Yang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‑Bioresources, Guangxi University, Nanning 530004, China.
| | - Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China.
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24
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Jackowska A, Gryko D. Vitamin B 12 Derivatives Suitably Tailored for the Synthesis of Photolabile Conjugates. Org Lett 2021; 23:4940-4944. [PMID: 33794095 DOI: 10.1021/acs.orglett.1c00839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vitamin B12 conjugates are broadly studied in biological sciences. As light offers spatiotemporal control, we decided to develop a method for the preparation of vitamin B12 conjugates that release tethered molecules upon exposure to light. Herein, we report vitamin B12 derivatives possessing a photolabile linker suitable for conjugation with amines, azides, and alkynes. The potential applications of such conjugates are broad and include the delivery of drugs, labels, and imaging agents to their place of action and spatiotemporal release.
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Affiliation(s)
- Agnieszka Jackowska
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Dorota Gryko
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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25
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Incaviglia I, Frutiger A, Blickenstorfer Y, Treindl F, Ammirati G, Lüchtefeld I, Dreier B, Plückthun A, Vörös J, Reichmuth AM. An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells. ACS Sens 2021; 6:1572-1582. [PMID: 33759497 DOI: 10.1021/acssensors.0c02480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In recent years, cell-based assays have been frequently used in molecular interaction analysis. Cell-based assays complement traditional biochemical and biophysical methods, as they allow for molecular interaction analysis, mode of action studies, and even drug screening processes to be performed under physiologically relevant conditions. In most cellular assays, biomolecules are usually labeled to achieve specificity. In order to overcome some of the drawbacks associated with label-based assays, we have recently introduced "cell-based molography" as a biosensor for the analysis of specific molecular interactions involving native membrane receptors in living cells. Here, we expand this assay to cytosolic protein-protein interactions. First, we created a biomimetic membrane receptor by tethering one cytosolic interaction partner to the plasma membrane. The artificial construct is then coherently arranged into a two-dimensional pattern within the cytosol of living cells. Thanks to the molographic sensor, the specific interactions between the coherently arranged protein and its endogenous interaction partners become visible in real time without the use of a fluorescent label. This method turns out to be an important extension of cell-based molography because it expands the range of interactions that can be analyzed by molography to those in the cytosol of living cells.
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Affiliation(s)
- Ilaria Incaviglia
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Yves Blickenstorfer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Fridolin Treindl
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Giulia Ammirati
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Ines Lüchtefeld
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Janos Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas M Reichmuth
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
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26
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Simultaneous readout of multiple FRET pairs using photochromism. Nat Commun 2021; 12:2005. [PMID: 33790271 PMCID: PMC8012603 DOI: 10.1038/s41467-021-22043-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/17/2021] [Indexed: 01/11/2023] Open
Abstract
Förster resonant energy transfer (FRET) is a powerful mechanism to probe associations in situ. Simultaneously performing more than one FRET measurement can be challenging due to the spectral bandwidth required for the donor and acceptor fluorophores. We present an approach to distinguish overlapping FRET pairs based on the photochromism of the donor fluorophores, even if the involved fluorophores display essentially identical absorption and emission spectra. We develop the theory underlying this method and validate our approach using numerical simulations. To apply our system, we develop rsAKARev, a photochromic biosensor for cAMP-dependent protein kinase (PKA), and combine it with the spectrally-identical biosensor EKARev, a reporter for extracellular signal-regulated kinase (ERK) activity, to deliver simultaneous readout of both activities in the same cell. We further perform multiplexed PKA, ERK, and calcium measurements by including a third, spectrally-shifted biosensor. Our work demonstrates that exploiting donor photochromism in FRET can be a powerful approach to simultaneously read out multiple associations within living cells. Performing multiple FRET measurements at once can be challenging. Here the authors report a method to discriminate between overlapping FRET pairs, even if the fluorophores display almost identical absorption and emission spectra, based on the photochromism of the donor fluorophores.
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27
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Yano S, Tazawa H, Kishimoto H, Kagawa S, Fujiwara T, Hoffman RM. Real-Time Fluorescence Image-Guided Oncolytic Virotherapy for Precise Cancer Treatment. Int J Mol Sci 2021; 22:E879. [PMID: 33477279 PMCID: PMC7830621 DOI: 10.3390/ijms22020879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/22/2022] Open
Abstract
Oncolytic virotherapy is one of the most promising, emerging cancer therapeutics. We generated three types of telomerase-specific replication-competent oncolytic adenovirus: OBP-301; a green fluorescent protein (GFP)-expressing adenovirus, OBP-401; and Killer-Red-armed OBP-301. These oncolytic adenoviruses are driven by the human telomerase reverse transcriptase (hTERT) promoter; therefore, they conditionally replicate preferentially in cancer cells. Fluorescence imaging enables visualization of invasion and metastasis in vivo at the subcellular level; including molecular dynamics of cancer cells, resulting in greater precision therapy. In the present review, we focused on fluorescence imaging applications to develop precision targeting for oncolytic virotherapy. Cell-cycle imaging with the fluorescence ubiquitination cell cycle indicator (FUCCI) demonstrated that combination therapy of an oncolytic adenovirus and a cytotoxic agent could precisely target quiescent, chemoresistant cancer stem cells (CSCs) based on decoying the cancer cells to cycle to S-phase by viral treatment, thereby rendering them chemosensitive. Non-invasive fluorescence imaging demonstrated that complete tumor resection with a precise margin, preservation of function, and prevention of distant metastasis, was achieved with fluorescence-guided surgery (FGS) with a GFP-reporter adenovirus. A combination of fluorescence imaging and laser ablation using a KillerRed-protein reporter adenovirus resulted in effective photodynamic cancer therapy (PDT). Thus, imaging technology and the designer oncolytic adenoviruses may have clinical potential for precise cancer targeting by indicating the optimal time for administering therapeutic agents; accurate surgical guidance for complete resection of tumors; and precise targeted cancer-specific photosensitization.
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Affiliation(s)
- Shuya Yano
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (H.K.); (S.K.); (T.F.)
- Center for Graduate Medical Education, Okayama University Hospital, Okayama 700-8558, Japan
| | - Hiroshi Tazawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (H.K.); (S.K.); (T.F.)
- Center of Innovative Clinical Medicine, Okayama University Hospital, Okayama 700-8558, Japan
| | - Hiroyuki Kishimoto
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (H.K.); (S.K.); (T.F.)
| | - Shunsuke Kagawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (H.K.); (S.K.); (T.F.)
- Minimally Invasive Therapy Center, Okayama University Hospital, Okayama 700-8558, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (H.K.); (S.K.); (T.F.)
| | - Robert M. Hoffman
- AntiCancer, Inc., San Diego, CA 92111, USA;
- Department of Surgery, University of California, San Diego, CA 92093, USA
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28
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Optogenetic Imaging of Protein Activity Using Two-Photon Fluorescence Lifetime Imaging Microscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:295-308. [PMID: 33398821 DOI: 10.1007/978-981-15-8763-4_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Spatiotemporal dynamics of cellular proteins, including protein-protein interactions and conformational changes, is essential for understanding cellular functions such as synaptic plasticity, cell motility, and cell division. One of the best ways to understand the mechanisms of signal transduction is to visualize protein activity with high spatiotemporal resolution in living cells within tissues. Optogenetic probes such as fluorescent proteins, in combination with Förster Resonance Energy Transfer (FRET) techniques, enable the measurement of protein-protein interactions and conformational changes in response to signaling events in living cells. Of the various FRET detection systems, two-photon fluorescence lifetime imaging microscopy (2pFLIM) is one of the methods best suited to monitoring FRET in subcellular compartments of living cells located deep within tissues, such as brain slices. This review will introduce the principle of 2pFLIM-FRET and the use of chromoproteins for imaging intracellular protein activities and protein-protein interactions. Also, we will discuss two examples of 2pFLIM-FRET application: imaging actin polymerization in synapses of hippocampal neurons in brain sections and detecting small GTPase Cdc42 activity in astrocytes.
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29
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Live Cell Imaging Using Riboswitch-Spinach tRNA Fusions as Metabolite-Sensing Fluorescent Biosensors. Methods Mol Biol 2021; 2323:121-140. [PMID: 34086278 DOI: 10.1007/978-1-0716-1499-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The development of fluorescent biosensors is motivated by the desire to monitor cellular metabolite levels in real time. Most genetically encodable fluorescent biosensors are based on receptor proteins fused to fluorescent protein domains. More recently, small molecule-binding riboswitches have been adapted for use as fluorescent biosensors through fusion to the in vitro selected Spinach aptamer, which binds a profluorescent, cell-permeable small molecule mimic of the GFP chromophore, DFHBI. Here we describe methods to prepare and analyze riboswitch-Spinach tRNA fusions for ligand-dependent activation of fluorescence in vivo. Example procedures describe the use of the Vc2-Spinach tRNA biosensor to monitor perturbations in cellular levels of cyclic di-GMP using either fluorescence microscopy or flow cytometry. In this updated chapter, we have added procedures on using biosensors in flow cytometry to detect exogenously added compounds. The relative ease of cloning and imaging of these biosensors, as well as their modular nature, should make this method appealing to other researchers interested in utilizing riboswitch-based biosensors for metabolite sensing.
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30
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Keyes J, Mehta S, Zhang J. Strategies for Multiplexed Biosensor Imaging to Study Intracellular Signaling Networks. Methods Mol Biol 2021; 2350:1-20. [PMID: 34331275 PMCID: PMC8580745 DOI: 10.1007/978-1-0716-1593-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Signal transduction processes are a necessary component of multicellular life, and their dysregulation is the basis for a host of syndromes and diseases. Thus, it is imperative that we discover the complex details of how signal transduction processes result in specific cellular outcomes. One of the primary mechanisms of regulation over signaling pathways is through spatiotemporal control. However, traditional methods are limited in their ability to reveal such details. To overcome these limitations, researchers have developed a variety of genetically encodable, fluorescent protein-based biosensors to study these dynamic processes in real time in living cells. Due to the complexities and interconnectedness of signaling pathways, it is thus desirable to use multiple biosensors in individual cells to better elucidate the relationships between signaling pathways. However, multiplexed imaging with such biosensors has been historically difficult. Nevertheless, recent developments in designs and multiplexing strategies have led to vast improvements in our capabilities. In this review, we provide perspectives on the recently developed biosensor designs and multiplexing strategies that are available for multiplexed imaging of signal transduction pathways.
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Affiliation(s)
- Jeremiah Keyes
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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31
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Khrenova MG, Mulashkin FD, Bulavko ES, Zakharova TM, Nemukhin AV. Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores. J Chem Inf Model 2020; 60:6288-6297. [PMID: 33206518 DOI: 10.1021/acs.jcim.0c01028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a quantitative structure-property relationship (QSPR) model for prediction of spectral tuning in cyan, green, orange, and red fluorescent proteins, which are engineered by motifs of the green fluorescent protein. Protein variants, in which their chromophores are involved in the π-stacking interaction with amino acid residues tyrosine, phenylalanine, and histidine, are prospective markers useful in bioimaging and super-resolution microscopy. In this work, we constructed training sets of the π-stacked complexes of four fluorescent protein chromophores (of the green, orange, red, and cyan series) with various substituted benzenes and imidazoles and tested the use of dipole moment variation upon excitation (DMV) as a descriptor to evaluate the vertical excitation energies in these systems. To validate this approach, we computed and analyzed electron density distributions of the π-stacked complexes and correlated the QSPR predictions with the reference values of the transition energies obtained using the high-level ab initio quantum chemistry methods. According to our results, the use of the DMV descriptor allows one to predict excitation energies in the π-stacked complexes with errors not exceeding 0.1 eV, which makes this model a practically useful tool in the development of efficient fluorescent markers for in vivo imaging.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Fedor D Mulashkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Egor S Bulavko
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Tatiana M Zakharova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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32
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Ma M, Bordignon P, Dotto GP, Pelet S. Visualizing cellular heterogeneity by quantifying the dynamics of MAPK activity in live mammalian cells with synthetic fluorescent biosensors. Heliyon 2020; 6:e05574. [PMID: 33319088 PMCID: PMC7723811 DOI: 10.1016/j.heliyon.2020.e05574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Mitogen-Activated Protein Kinases (MAPKs) control a wide array of cellular functions by transducing extracellular information into defined biological responses. In order to understand how these pathways are regulated, dynamic single cell measurements are highly needed. Fluorescence microscopy is well suited to perform these measurements. However, more dynamic and sensitive biosensors that allow the quantification of signaling activity in living mammalian cells are required. We have engineered a synthetic fluorescent substrate for human MAPKs (ERK, JNK and p38) that relocates from the nucleus to the cytoplasm when phosphorylated by the kinases. We demonstrate that this reporter displays an improved response compared to other relocation biosensors. This assay allows to monitor the heterogeneity in the MAPK response in a population of isogenic cells, revealing pulses of ERK activity upon a physiological EGFR stimulation. We show applicability of this approach to the analysis of multiple cancer cell lines and primary cells as well as its application in vivo to developing tumors. Using this ERK biosensor, dynamic single cell measurements with high temporal resolution can be obtained. These MAPK reporters can be widely applied to the analysis of molecular mechanisms of MAPK signaling in healthy and diseased state, in cell culture assays or in vivo.
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Affiliation(s)
- Min Ma
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Department of Biochemistry, University of Lausanne, Switzerland
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, Switzerland
| | | | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
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33
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Wei M, Lin P, Chen Y, Lee JY, Zhang L, Li F, Ling D. Applications of ion level nanosensors for neuroscience research. Nanomedicine (Lond) 2020; 15:2871-2881. [PMID: 33252311 DOI: 10.2217/nnm-2020-0320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ion activities are tightly associated with brain physiology, such as intracranial cell membrane potential, neural activity and neuropathology. Thus, monitoring the ion levels in the brain is of great significance in neuroscience research. Recently, nanosensors have emerged as powerful tools for monitoring brain ion levels and dynamics. With controllable structures and functions, nanosensors have been intensively used for monitoring neural activity and cell function and can be used in disease diagnosis. Here, we summarize the recent advances in the design and application of ion level nanosensors at different physiological levels, aiming to draw a connection of the interrelated intracranial ion activities. Furthermore, perspectives on the rationally designed ion level nanosensors in understanding the brain functions are highlighted.
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Affiliation(s)
- Min Wei
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peihua Lin
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Chen
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ji Young Lee
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingxiao Zhang
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fangyuan Li
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Daishun Ling
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Key Laboratory of Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310058, China
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Steinegger A, Wolfbeis OS, Borisov SM. Optical Sensing and Imaging of pH Values: Spectroscopies, Materials, and Applications. Chem Rev 2020; 120:12357-12489. [PMID: 33147405 PMCID: PMC7705895 DOI: 10.1021/acs.chemrev.0c00451] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 12/13/2022]
Abstract
This is the first comprehensive review on methods and materials for use in optical sensing of pH values and on applications of such sensors. The Review starts with an introduction that contains subsections on the definition of the pH value, a brief look back on optical methods for sensing of pH, on the effects of ionic strength on pH values and pKa values, on the selectivity, sensitivity, precision, dynamic ranges, and temperature dependence of such sensors. Commonly used optical sensing schemes are covered in a next main chapter, with subsections on methods based on absorptiometry, reflectometry, luminescence, refractive index, surface plasmon resonance, photonic crystals, turbidity, mechanical displacement, interferometry, and solvatochromism. This is followed by sections on absorptiometric and luminescent molecular probes for use pH in sensors. Further large sections cover polymeric hosts and supports, and methods for immobilization of indicator dyes. Further and more specific sections summarize the state of the art in materials with dual functionality (indicator and host), nanomaterials, sensors based on upconversion and 2-photon absorption, multiparameter sensors, imaging, and sensors for extreme pH values. A chapter on the many sensing formats has subsections on planar, fiber optic, evanescent wave, refractive index, surface plasmon resonance and holography based sensor designs, and on distributed sensing. Another section summarizes selected applications in areas, such as medicine, biology, oceanography, bioprocess monitoring, corrosion studies, on the use of pH sensors as transducers in biosensors and chemical sensors, and their integration into flow-injection analyzers, microfluidic devices, and lab-on-a-chip systems. An extra section is devoted to current challenges, with subsections on challenges of general nature and those of specific nature. A concluding section gives an outlook on potential future trends and perspectives.
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Affiliation(s)
- Andreas Steinegger
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Otto S. Wolfbeis
- Institute
of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany
| | - Sergey M. Borisov
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
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Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies. Proc Natl Acad Sci U S A 2020; 117:30476-30487. [PMID: 33214152 DOI: 10.1073/pnas.2007443117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-concept to perform single-particle tracking on a range of GFP proteins expressed in live cells, neurons, and small organisms. We next expressed highly specialized nanobodies that target conformation-specific endogenous β2-adrenoreceptor (β2-AR) in neurosecretory cells, unveiling real-time mobility behaviors of activated and inactivated endogenous conformers during agonist treatment in living cells. We showed that activated β2-AR (Nb80) is highly immobile and organized in nanoclusters. The Gαs-GPCR complex detected with Nb37 displayed higher mobility with surprisingly similar nanoclustering dynamics to that of Nb80. Activated conformers are highly sensitive to dynamin inhibition, suggesting selective targeting for endocytosis. Inactivated β2-AR (Nb60) molecules are also largely immobile but relatively less sensitive to endocytic blockade. Expression of single-domain nanobodies therefore provides a unique opportunity to capture highly transient changes in the dynamic nanoscale organization of endogenous proteins.
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36
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Recent advances in aptasensors for mycotoxin detection: On the surface and in the colloid. Talanta 2020; 223:121729. [PMID: 33303172 DOI: 10.1016/j.talanta.2020.121729] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/08/2023]
Abstract
Mycotoxins are a great potential threat to human health, and the progress in the development of mycotoxin detection methods is of an escalating importance with the increasing emphasis on food safety. Aptamer, performing the same function as antibody in specific binding with targets, exhibits profound potential in biosensing since its debut in 1990. Recent years have witnessed the rapid development of aptasensors for mycotoxin detection with the achievement of ultralow limit of detection and high sensitivity in the lab. However, there is still no officially approved aptasensing methods in mycotoxin detection application. In order to provide researchers with inspirations in the design and development of aptasensors for mycotoxin detection, we divide these aptasensors into two types, namely "on the surface" and "in the colloid", according to the location where the key sensing reaction occurs. We also systematically review aptasensors reported in the past 5 years under the abovementioned criterion of classification, and compare the advantages and disadvantages of each kind of aptasensors. Finally, we discuss prospective directions in the development of aptasensors for mycotoxin detection. This paper will offer insight and motivation to practitioners working on the research and practical application of aptasensors in the detection of mycotoxins and other substances.
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37
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Salimiyan Rizi K, Aryan E, Meshkat Z, Ranjbar G, Sankian M, Ghazvini K, Farsiani H, Pourianfar HR, Rezayi M. The overview and perspectives of biosensors and Mycobacterium tuberculosis: A systematic review. J Cell Physiol 2020; 236:1730-1750. [PMID: 32930412 DOI: 10.1002/jcp.30007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) is referred to as a "consumption" or phthisis, which has been a fatal human disease for thousands of years. Mycobacterium tuberculosis (M. tb) might have been responsible for the death of more humans than any other bacterial pathogens. Therefore, the rapid diagnosis of this bacterial infection plays a pivotal role in the timely and appropriate treatment of the patients, as well as the prevention of disease spread. More than 98% of TB cases are reported in developing countries, and due to the lack of well-equipped and specialized diagnostic laboratories, development of effective diagnostic methods based on biosensors is essential for this bacterium. In this review, original articles published in English were retrieved from multiple databases, such as PubMed, Scopus, Google Scholar, Science Direct, and Cochrane Library during January 2010-October 2019. In addition, the reference lists of the articles were also searched. Among 109 electronically searched citations, 42 articles met the inclusion criteria. The highest potential and wide usage of biosensors for the diagnosis of M. tb and its drug resistance belonged to DNA electrochemical biosensors (isoniazid and rifampin strains). Use of biosensors is expanding for the detection of resistant strains of anti-TB antibiotics with high sensitivity and accuracy, while the speed of these sensory methods is considered essential as well. Furthermore, the lowest limit of detection (0.9 fg/ml) from an electrochemical DNA biosensor was based on graphene-modified iron-oxide chitosan hybrid deposited on fluorine tin oxide for the MPT64 antigen target. According to the results, the most common methods used for M. tb detection include acid-fast staining, cultivation, and polymerase chain reaction (PCR). Although molecular techniques (e.g., PCR and real-time PCR) are rapid and sensitive, they require sophisticated laboratory and apparatuses, as well as skilled personnel and expertise in the commentary of the results. Biosensors are fast, valid, and cost-efficient diagnostic method, and the improvement of their quality is of paramount importance in resource-constrained settings.
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Affiliation(s)
- Kobra Salimiyan Rizi
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Aryan
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Golnaz Ranjbar
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Division of Immunobiochemistry, Immunology Research Centre, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Farsiani
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid R Pourianfar
- Research Department of Industrial Fungi Biotechnology, Research Institute for Industrial Biotechnology, Academic Centre for Education, Culture and Research [ACECR]-Khorasan Razavi Province Branch, Mashhad, Iran
| | - Majid Rezayi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Bhattacharya B, Roy D, Dey S, Puthuvakkal A, Bhunia S, Mondal S, Chowdhury R, Bhattacharya M, Mandal M, Manoj K, Mandal PK, Reddy CM. Mechanical‐Bending‐Induced Fluorescence Enhancement in Plastically Flexible Crystals of a GFP Chromophore Analogue. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Biswajit Bhattacharya
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Debjit Roy
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Somnath Dey
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Anisha Puthuvakkal
- Photosciences and Photonics Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - Surojit Bhunia
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Saikat Mondal
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Rituparno Chowdhury
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Manjima Bhattacharya
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Mrinal Mandal
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Kochunnoonny Manoj
- Photosciences and Photonics Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - Prasun K. Mandal
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - C. Malla Reddy
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
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39
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Bhattacharya B, Roy D, Dey S, Puthuvakkal A, Bhunia S, Mondal S, Chowdhury R, Bhattacharya M, Mandal M, Manoj K, Mandal PK, Reddy CM. Mechanical-Bending-Induced Fluorescence Enhancement in Plastically Flexible Crystals of a GFP Chromophore Analogue. Angew Chem Int Ed Engl 2020; 59:19878-19883. [PMID: 32667123 DOI: 10.1002/anie.202007760] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Indexed: 01/25/2023]
Abstract
Single crystals of optoelectronic materials that respond to external stimuli, such as mechanical, light, or heat, are immensely attractive for next generation smart materials. Here we report single crystals of a green fluorescent protein (GFP) chromophore analogue with irreversible mechanical bending and associated unusual enhancement of the fluorescence, which is attributed to the strained molecular packing in the perturbed region. Soft crystalline materials with such fluorescence intensity modulations occurring in response to mechanical stimuli under ambient pressure conditions will have potential implications for the design of technologically relevant tunable fluorescent materials.
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Affiliation(s)
- Biswajit Bhattacharya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Debjit Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Somnath Dey
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Anisha Puthuvakkal
- Photosciences and Photonics, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - Surojit Bhunia
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Saikat Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Rituparno Chowdhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Manjima Bhattacharya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Mrinal Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Kochunnoonny Manoj
- Photosciences and Photonics, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - Prasun K Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - C Malla Reddy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
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40
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Werley CA, Boccardo S, Rigamonti A, Hansson EM, Cohen AE. Multiplexed Optical Sensors in Arrayed Islands of Cells for multimodal recordings of cellular physiology. Nat Commun 2020; 11:3881. [PMID: 32753572 PMCID: PMC7403318 DOI: 10.1038/s41467-020-17607-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Cells typically respond to chemical or physical perturbations via complex signaling cascades which can simultaneously affect multiple physiological parameters, such as membrane voltage, calcium, pH, and redox potential. Protein-based fluorescent sensors can report many of these parameters, but spectral overlap prevents more than ~4 modalities from being recorded in parallel. Here we introduce the technique, MOSAIC, Multiplexed Optical Sensors in Arrayed Islands of Cells, where patterning of fluorescent sensor-encoding lentiviral vectors with a microarray printer enables parallel recording of multiple modalities. We demonstrate simultaneous recordings from 20 sensors in parallel in human embryonic kidney (HEK293) cells and in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and we describe responses to metabolic and pharmacological perturbations. Together, these results show that MOSAIC can provide rich multi-modal data on complex physiological responses in multiple cell types.
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Affiliation(s)
- Christopher A Werley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Q-State Biosciences, Cambridge, MA, 02139, USA
| | - Stefano Boccardo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Nobel Biocare AG, Kloten, Switzerland
| | - Alessandra Rigamonti
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
| | - Emil M Hansson
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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41
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González-Ruiz V, Rajesh J, Olives AI, Rocchi D, Gómez-Carpintero J, González JF, Sridharan V, Martín MA, Menéndez JC. Antioxidants as Molecular Probes: Structurally Novel Dihydro- m-Terphenyls as Turn-On Fluorescence Chemodosimeters for Biologically Relevant Oxidants. Antioxidants (Basel) 2020; 9:antiox9070605. [PMID: 32664230 PMCID: PMC7402136 DOI: 10.3390/antiox9070605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 11/16/2022] Open
Abstract
One interesting aspect of antioxidant organic molecules is their use as probes for the detection and quantitation of biologically relevant reactive oxidant species (ROS). In this context, a small library of dihydroterphenyl derivatives has been synthesised and studied as fluorescent chemodosimeters for detecting reactive oxygen species and hypochlorite. The fluorescence quantum yields of these molecules are negligible, while the corresponding aromatized compounds formed upon oxidation show moderate to high native fluorescence, depending on their structures. The fluorescence signal is quickly developed in the presence of trace amounts of the probe and the analytes in acetonitrile media at room temperature, with good analytical figures. ROS detection in aqueous media required incubation at 37 °C in the presence of horseradish peroxidase, and was applied to glucose quantitation by coupling glucose oxidation by O2 to fluorescence detection of H2O2. The mild reaction conditions and sensitive fluorescent response lead us to propose dihydroterphenyls with an embedded anthranilate moiety as chemosensors/chemodosimeters for ROS detection.
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Affiliation(s)
- Víctor González-Ruiz
- Unidad de Química Analítica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (V.G.-R.); (J.R.); (A.I.O.)
| | - Jegathalaprathaban Rajesh
- Unidad de Química Analítica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (V.G.-R.); (J.R.); (A.I.O.)
| | - Ana I. Olives
- Unidad de Química Analítica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (V.G.-R.); (J.R.); (A.I.O.)
| | - Damiano Rocchi
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (D.R.); (J.G.-C.); (J.F.G.)
| | - Jorge Gómez-Carpintero
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (D.R.); (J.G.-C.); (J.F.G.)
| | - Juan F. González
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (D.R.); (J.G.-C.); (J.F.G.)
| | - Vellaisamy Sridharan
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), District-Samba, Jammu-181143, J&K, India;
| | - M. Antonia Martín
- Unidad de Química Analítica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (V.G.-R.); (J.R.); (A.I.O.)
- Correspondence: (M.A.M.); (J.C.M.)
| | - J. Carlos Menéndez
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (D.R.); (J.G.-C.); (J.F.G.)
- Correspondence: (M.A.M.); (J.C.M.)
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42
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Design of fluorescent protein-based sensors through a general protection-deprotection strategy. Methods Enzymol 2020; 640:63-82. [PMID: 32560806 DOI: 10.1016/bs.mie.2020.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Engineered fluorescent proteins have been extensively used in biological research for the study of gene expression, protein function and trafficking, and protein-protein interactions. In addition, fluorescent proteins have also been engineered to act as biosensing agents to detect intracellular signaling molecules and other small-molecule metabolites. Although they have been engineered extensively to achieve novel properties, fluorescent proteins are traditionally modified using the 20 canonical amino acids. This limits the number of functional groups that are available to the design and construction of novel fluorescent proteins. The expansion of the genetic code through the incorporation of noncanonical amino acids presents an opportunity to add new functionalities with the intent of modifying chemical and physical properties of fluorescent proteins. Herein we provide a general procedure for the site-specific incorporation of noncanonical amino acids into fluorescent proteins in live cells. We will also discuss a noncanonical amino acid-containing fluorescent protein sensor that is based on a general protection-deprotection design strategy, for the selective detection and quantification of Hg2+.
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43
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Kostyuk AI, Kokova AD, Podgorny OV, Kelmanson IV, Fetisova ES, Belousov VV, Bilan DS. Genetically Encoded Tools for Research of Cell Signaling and Metabolism under Brain Hypoxia. Antioxidants (Basel) 2020; 9:E516. [PMID: 32545356 PMCID: PMC7346190 DOI: 10.3390/antiox9060516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 02/08/2023] Open
Abstract
Hypoxia is characterized by low oxygen content in the tissues. The central nervous system (CNS) is highly vulnerable to a lack of oxygen. Prolonged hypoxia leads to the death of brain cells, which underlies the development of many pathological conditions. Despite the relevance of the topic, different approaches used to study the molecular mechanisms of hypoxia have many limitations. One promising lead is the use of various genetically encoded tools that allow for the observation of intracellular parameters in living systems. In the first part of this review, we provide the classification of oxygen/hypoxia reporters as well as describe other genetically encoded reporters for various metabolic and redox parameters that could be implemented in hypoxia studies. In the second part, we discuss the advantages and disadvantages of the primary hypoxia model systems and highlight inspiring examples of research in which these experimental settings were combined with genetically encoded reporters.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Koltzov Institute of Developmental Biology, 119334 Moscow, Russia
| | - Ilya V. Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Elena S. Fetisova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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44
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Tressler CM, Zondlo NJ. Perfluoro- tert-Butyl Hydroxyprolines as Sensitive, Conformationally Responsive Molecular Probes: Detection of Protein Kinase Activity by 19F NMR. ACS Chem Biol 2020; 15:1096-1103. [PMID: 32125821 DOI: 10.1021/acschembio.0c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
19F NMR spectroscopy provides the ability to quantitatively analyze single species in complex solutions but is often limited by the modest sensitivity inherent to NMR. 4R- and 4S-Perfluoro-tert-buyl hydroxyproline contain 9 equivalent fluorines, in amino acids with strong conformational preferences. In order to test the ability to use these amino acids as sensitive probes of protein modifications, the perfluoro-tert-buyl hydroxyprolines were incorporated into substrate peptides of the protein kinases PKA and Akt. Peptides containing each diastereomeric proline were rapidly phosphorylated by each protein kinase and exhibited 19F chemical shift changes as a result of phosphorylation. The sensitivity of the perfluoro-tert-butyl group allowed quantitative analysis of the kinetics of phosphorylation over three half-lives at single-digit micromolar concentrations of each species. The distinct conformational preferences of these amino acids allowed the optimization of the substrate with a conformationally matched amino acid, in order to maximize the rate of phosphorylation. PKA preferred the 4R-amino acid at the -1 position, whereas the closely related AGC kinase Akt preferred the 4S-amino acid. These data, combined with analysis of structures of the Michaelis complexes of these kinases in the PDB, suggest that PKA recognizes the PPII conformation at the P-1 position relative to the phosphorylation site, while Akt/PKB recognizes an extended conformation at this position. These results suggest that conformational targeting may be employed to increase specificity in recognition by protein kinases. Perfluoro-tert-butyl hydroxyprolines were applied to the real-time detection and quantification of PKA activity and inhibition of PKA activity in HeLa cell extracts via 19F NMR spectroscopy. The coupling of proline ring pucker with main chain conformation suggests broad application of perfluoro-tert-butyl hydroxyprolines in molecular sensing and imaging.
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Affiliation(s)
- Caitlin M. Tressler
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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Santos EM, Berbasova T, Wang W, Salmani RE, Sheng W, Vasileiou C, Geiger JH, Borhan B. Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging. Chembiochem 2020; 21:723-729. [PMID: 31482666 PMCID: PMC7379159 DOI: 10.1002/cbic.201900428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 12/25/2022]
Abstract
A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.
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Affiliation(s)
- Elizabeth M. Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Tetyana Berbasova
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Wenjing Wang
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | | | - Wei Sheng
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - James H. Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
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46
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Lee SN, Choi JH, Cho HY, Choi JW. Metallic Nanoparticle-Based Optical Cell Chip for Nondestructive Monitoring of Intra/Extracellular Signals. Pharmaceutics 2020; 12:pharmaceutics12010050. [PMID: 31936079 PMCID: PMC7022866 DOI: 10.3390/pharmaceutics12010050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/31/2019] [Accepted: 01/06/2020] [Indexed: 12/23/2022] Open
Abstract
The biosensing platform is noteworthy for high sensitivity and precise detection of target analytes, which are related to the status of cells or specific diseases. The modification of the transducers with metallic nanoparticles (MNPs) has attracted attention owing to excellent features such as improved sensitivity and selectivity. Moreover, the incorporation of MNPs into biosensing systems may increase the speed and the capability of the biosensors. In this review, we introduce the current progress of the developed cell-based biosensors, cell chip, based on the unique physiochemical features of MNPs. Mainly, we focus on optical intra/extracellular biosensing methods, including fluorescence, localized surface plasmon resonance (LSPR), and surface-enhanced Raman spectroscopy (SERS) based on the coupling of MNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of new MNP-based cell chip platforms for pharmaceutical applications such as drug screening and toxicological tests in the near future.
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Affiliation(s)
- Sang-Nam Lee
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-Gu, Seoul 04107, Korea; (S.-N.L.); (J.-H.C.)
- Uniance Gene Inc., 1107 Teilhard Hall, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Jin-Ha Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-Gu, Seoul 04107, Korea; (S.-N.L.); (J.-H.C.)
| | - Hyeon-Yeol Cho
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-Gu, Seoul 04107, Korea; (S.-N.L.); (J.-H.C.)
- Correspondence: (H.-Y.C.); (J.-W.C.); Tel.: +82-2-705-8480 (J.-W.C.)
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-Gu, Seoul 04107, Korea; (S.-N.L.); (J.-H.C.)
- Correspondence: (H.-Y.C.); (J.-W.C.); Tel.: +82-2-705-8480 (J.-W.C.)
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47
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Pope JR, Johnson RL, Jamieson WD, Worthy HL, Kailasam S, Ahmed RD, Taban I, Auhim HS, Watkins DW, Rizkallah PJ, Castell OK, Jones DD. Association of Fluorescent Protein Pairs and Its Significant Impact on Fluorescence and Energy Transfer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 8:2003167. [PMID: 33437587 PMCID: PMC7788595 DOI: 10.1002/advs.202003167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 06/01/2023]
Abstract
Fluorescent proteins (FPs) are commonly used in pairs to monitor dynamic biomolecular events through changes in proximity via distance dependent processes such as Förster resonance energy transfer (FRET). The impact of FP association is assessed by predicting dimerization sites in silico and stabilizing the dimers by bio-orthogonal covalent linkages. In each tested case dimerization changes inherent fluorescence, including FRET. GFP homodimers demonstrate synergistic behavior with the dimer being brighter than the sum of the monomers. The homodimer structure reveals the chromophores are close with favorable transition dipole alignments and a highly solvated interface. Heterodimerization (GFP with Venus) results in a complex with ≈87% FRET efficiency, significantly below the 99.7% efficiency predicted. A similar efficiency is observed when the wild-type FPs are fused to a naturally occurring protein-protein interface system. GFP complexation with mCherry results in loss of mCherry fluorescence. Thus, simple assumptions used when monitoring interactions between proteins via FP FRET may not always hold true, especially under conditions whereby the protein-protein interactions promote FP interaction.
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Affiliation(s)
- Jacob R. Pope
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | - Rachel L. Johnson
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | | | - Harley L. Worthy
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
- Present address:
Henry Wellcome Building for BiocatalysisBiosciencesUniversity of ExeterExeterEX4 4QDUK
| | - Senthilkumar Kailasam
- McGill University and Genome Quebec Innovation CentreMontrealQuebecH3A 0G1Canada
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
| | - Rochelle D. Ahmed
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | - Ismail Taban
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
| | - Husam Sabah Auhim
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
- Department of BiologyCollege of ScienceUniversity of BaghdadBaghdadIraq
| | - Daniel W. Watkins
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
- Present address:
School of BiochemistryUniversity of BristolBristolBS8 1QUUK
| | | | | | - D. Dafydd Jones
- Molecular BiosciencesSchool of BiosciencesCardiff UniversityCardiffCF10 3AXUK
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Blázquez-Moraleja A, Sáenz-de-Santa María I, Chiara MD, Álvarez-Fernández D, García-Moreno I, Prieto-Montero R, Martínez-Martínez V, López Arbeloa I, Chiara JL. Shedding light on the mitochondrial matrix through a functional membrane transporter. Chem Sci 2019; 11:1052-1065. [PMID: 34084361 PMCID: PMC8146229 DOI: 10.1039/c9sc04852a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The first fluorescent probes that are actively channeled into the mitochondrial matrix by a specific mitochondrial membrane transporter in living cells have been developed. The new functional probes (BCT) have a minimalist structural design based on the highly efficient and photostable BODIPY chromophore and carnitine as a biotargeting element. Both units are orthogonally bonded through the common boron atom, thus avoiding the use of complex polyatomic connectors. In contrast to known mitochondria-specific dyes, BCTs selectively label these organelles regardless of their transmembrane potential and in an enantioselective way. The obtained experimental evidence supports carnitine–acylcarnitine translocase (CACT) as the key transporter protein for BCTs, which behave therefore as acylcarnitine biomimetics. This simple structural design can be readily extended to other structurally diverse starting F-BODIPYs to obtain BCTs with varied emission wavelengths along the visible and NIR spectral regions and with multifunctional capabilities. BCTs are the first fluorescent derivatives of carnitine to be used in cell microscopy and stand as promising research tools to explore the role of the carnitine shuttle system in cancer and metabolic diseases. Extension of this approach to other small-molecule mitochondrial transporters is envisaged. A BODIPY derivative of carnitine enters mitochondria regardless of their membrane potential and in an enantioselective way through a specific mitochondrial membrane transporter in living cells.![]()
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Affiliation(s)
| | - Ines Sáenz-de-Santa María
- Instituto de Investigación Sanitaria del Principado de Asturias, Instituto de Oncología del Principado de Asturias (IUOPA), CIBERONC, Universidad de Oviedo, Hospital Central de Asturias 33011 Oviedo Spain
| | - María D Chiara
- Instituto de Investigación Sanitaria del Principado de Asturias, Instituto de Oncología del Principado de Asturias (IUOPA), CIBERONC, Universidad de Oviedo, Hospital Central de Asturias 33011 Oviedo Spain
| | | | | | - Ruth Prieto-Montero
- Departamento de Química Física, Universidad del País Vasco UPV-EHU, Facultad de Ciencia y Tecnología Apartado 644 48080 Bilbao Spain
| | - Virginia Martínez-Martínez
- Departamento de Química Física, Universidad del País Vasco UPV-EHU, Facultad de Ciencia y Tecnología Apartado 644 48080 Bilbao Spain
| | - Iñigo López Arbeloa
- Departamento de Química Física, Universidad del País Vasco UPV-EHU, Facultad de Ciencia y Tecnología Apartado 644 48080 Bilbao Spain
| | - Jose Luis Chiara
- Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3 28006 Madrid Spain
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Fluorescent Protein-Based Indicators for Functional Super-Resolution Imaging of Biomolecular Activities in Living Cells. Int J Mol Sci 2019; 20:ijms20225784. [PMID: 31744242 PMCID: PMC6887983 DOI: 10.3390/ijms20225784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022] Open
Abstract
Super-resolution light microscopy (SRM) offers a unique opportunity for diffraction-unlimited imaging of biomolecular activities in living cells. To realize such potential, genetically encoded indicators were developed recently from fluorescent proteins (FPs) that exhibit phototransformation behaviors including photoactivation, photoconversion, and photoswitching, etc. Super-resolution observations of biomolecule interactions and biochemical activities have been demonstrated by exploiting the principles of bimolecular fluorescence complementation (BiFC), points accumulation for imaging nanoscale topography (PAINT), and fluorescence fluctuation increase by contact (FLINC), etc. To improve functional nanoscopy with the technology of genetically encoded indicators, it is essential to fully decipher the photo-induced chemistry of FPs and opt for innovative indicator designs that utilize not only fluorescence intensity but also multi-parametric readouts such as phototransformation kinetics. In parallel, technical improvements to both the microscopy optics and image analysis pipeline are promising avenues to increase the sensitivity and versatility of functional SRM.
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50
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Ko S, Hwang B, Na JH, Lee J, Jung ST. Engineered Arabidopsis Blue Light Receptor LOV Domain Variants with Improved Quantum Yield, Brightness, and Thermostability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12037-12043. [PMID: 31581772 DOI: 10.1021/acs.jafc.9b05473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite remarkable contribution of green fluorescent protein and its variants for better understanding of various biological functions, its application for anaerobic microorganisms has been limited because molecular oxygen is essential for chromophore formation. To overcome the limitation, we engineered a plant-derived light, oxygen, or voltage (LOV) domain containing flavin mononucleotide for enhanced spectral properties. The resulting LOV variants exhibited improved fluorescence intensity (20 and 70% higher for SH3 and 70% for BR1, respectively) compared to iLOV, an LOV variant isolated in a previous study, and the quantum yields of the LOV variants (0.40 for SH3 and 0.45 for BR1) were also improved relative to that of iLOV (Q = 0.37). In addition to fluorescence intensity, the identified mutations of SH3 enabled an improved thermostability of the protein. The engineered LOV variants with enhanced spectral properties could provide a valuable tool for fluorescent molecular probes under anaerobic conditions.
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Affiliation(s)
- Sanghwan Ko
- Department of Biomedical Sciences, Graduate School of Medicine , Korea University , Seoul 02841 , Republic of Korea
- Department of Applied Chemistry , Kookmin University , Seoul 02707 , Republic of Korea
| | - Bora Hwang
- Department of Applied Chemistry , Kookmin University , Seoul 02707 , Republic of Korea
| | - Jung-Hyun Na
- Department of Applied Chemistry , Kookmin University , Seoul 02707 , Republic of Korea
- Division of Discovery and Optimization, New Drug Development Center , Osong Medical Innovation Foundation , Cheongju , Chungcheongbuk-do 28160 , Republic of Korea
| | - Jisun Lee
- Department of Biomedical Sciences, Graduate School of Medicine , Korea University , Seoul 02841 , Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine , Korea University , Seoul 02841 , Republic of Korea
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