1
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Mandrou E, Thomason PA, Paschke PI, Paul NR, Tweedy L, Insall RH. A Reliable System for Quantitative G-Protein Activation Imaging in Cancer Cells. Cells 2024; 13:1114. [PMID: 38994966 DOI: 10.3390/cells13131114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Fluorescence resonance energy transfer (FRET) biosensors have proven to be an indispensable tool in cell biology and, more specifically, in the study of G-protein signalling. The best method of measuring the activation status or FRET state of a biosensor is often fluorescence lifetime imaging microscopy (FLIM), as it does away with many disadvantages inherent to fluorescence intensity-based methods and is easily quantitated. Despite the significant potential, there is a lack of reliable FLIM-FRET biosensors, and the data processing and analysis workflows reported previously face reproducibility challenges. Here, we established a system in live primary mouse pancreatic ductal adenocarcinoma cells, where we can detect the activation of an mNeonGreen-Gαi3-mCherry-Gγ2 biosensor through the lysophosphatidic acid receptor (LPAR) with 2-photon time-correlated single-photon counting (TCSPC) FLIM. This combination gave a superior signal to the commonly used mTurquoise2-mVenus G-protein biosensor. This system has potential as a platform for drug screening, or to answer basic cell biology questions in the field of G-protein signalling.
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Affiliation(s)
- Elena Mandrou
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
| | | | - Peggy I Paschke
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
| | - Nikki R Paul
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
| | - Luke Tweedy
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Robert H Insall
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
- Division of Cell & Developmental Biology, University College London, London WC1E 6BT, UK
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2
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Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
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Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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3
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Nam KH, Xu Y. Structural Analysis of the Large Stokes Shift Red Fluorescent Protein tKeima. Molecules 2024; 29:2579. [PMID: 38893454 PMCID: PMC11173989 DOI: 10.3390/molecules29112579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The Keima family comprises large Stokes shift fluorescent proteins that are useful for dual-color fluorescence cross-correlation spectroscopy and multicolor imaging. The tKeima is a tetrameric large Stokes shift fluorescent protein and serves as the ancestor fluorescent protein for both dKeima and mKeima. The spectroscopic properties of tKeima have been previously reported; however, its structural basis and molecular properties have not yet been elucidated. In this study, we present the crystallographic results of the large Stokes shift fluorescent protein tKeima. The purified tKeima protein spontaneously crystallized after purification without further crystallization. The crystal structure of tKeima was determined at 3.0 Å resolution, revealing a β-barrel fold containing the Gln-Tyr-Gly chromophores mainly with cis-conformation. The tetrameric interfaces of tKeima were stabilized by numerous hydrogen bonds and salt-bridge interactions. These key residues distinguish the substituted residues in dKeima and mKeima. The key structure-based residues involved in the tetramer formation of tKeima provide insights into the generation of a new type of monomeric mKeima. This structural analysis expands our knowledge of the Keima family and provides insights into its protein engineering.
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Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
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4
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Kapitany V, Fatima A, Zickus V, Whitelaw J, McGhee E, Insall R, Machesky L, Faccio D. Single-sample image-fusion upsampling of fluorescence lifetime images. SCIENCE ADVANCES 2024; 10:eadn0139. [PMID: 38781345 PMCID: PMC11114222 DOI: 10.1126/sciadv.adn0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) provides detailed information about molecular interactions and biological processes. A major bottleneck for FLIM is image resolution at high acquisition speeds due to the engineering and signal-processing limitations of time-resolved imaging technology. Here, we present single-sample image-fusion upsampling, a data-fusion approach to computational FLIM super-resolution that combines measurements from a low-resolution time-resolved detector (that measures photon arrival time) and a high-resolution camera (that measures intensity only). To solve this otherwise ill-posed inverse retrieval problem, we introduce statistically informed priors that encode local and global correlations between the two "single-sample" measurements. This bypasses the risk of out-of-distribution hallucination as in traditional data-driven approaches and delivers enhanced images compared, for example, to standard bilinear interpolation. The general approach laid out by single-sample image-fusion upsampling can be applied to other image super-resolution problems where two different datasets are available.
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Affiliation(s)
- Valentin Kapitany
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - Areeba Fatima
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
| | - Vytautas Zickus
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
- Department of Laser Technologies, Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania
| | | | - Ewan McGhee
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
- Cancer Research UK, Beatson Institute, Glasgow, UK
| | | | | | - Daniele Faccio
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, UK
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5
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Lim SL, Liu J, Dupouy G, Singh G, Baudrey S, Yang L, Zhong JY, Chabouté ME, Lim BL. In planta imaging of pyridine nucleotides using second-generation fluorescent protein biosensors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38761168 DOI: 10.1111/tpj.16796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Redox changes of pyridine nucleotides in cellular compartments are highly dynamic and their equilibria are under the influence of various reducing and oxidizing reactions. To obtain spatiotemporal data on pyridine nucleotides in living plant cells, typical biochemical approaches require cell destruction. To date, genetically encoded fluorescent biosensors are considered to be the best option to bridge the existing technology gap, as they provide a fast, accurate, and real-time readout. However, the existing pyridine nucleotides genetically encoded fluorescent biosensors are either sensitive to pH change or slow in dissociation rate. Herein, we employed the biosensors which generate readouts that are pH stable for in planta measurement of NADH/NAD+ ratio and NADPH level. We generated transgenic Arabidopsis lines that express these biosensors in plastid stroma and cytosol of whole plants and pollen tubes under the control of CaMV 35S and LAT52 promoters, respectively. These transgenic biosensor lines allow us to monitor real-time dynamic changes in NADH/NAD+ ratio and NADPH level in the plastids and cytosol of various plant tissues, including pollen tubes, root hairs, and mesophyll cells, using a variety of fluorescent instruments. We anticipate that these valuable transgenic lines may allow improvements in plant redox biology studies.
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Affiliation(s)
- Shey-Li Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Jinhong Liu
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Gilles Dupouy
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Gaurav Singh
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Stéphanie Baudrey
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, UPR 9002, Strasbourg, 67000, France
| | - Lang Yang
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Jia Yi Zhong
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
- HKU Shenzhen Institute of Research and Innovation, Shenzhen, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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Carrillo R, Iwai K, Albertson A, Dang G, Christopher DA. Protein disulfide isomerase-9 interacts with the lumenal region of the transmembrane endoplasmic reticulum stress sensor kinase, IRE1, to modulate the unfolded protein response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1389658. [PMID: 38817940 PMCID: PMC11137178 DOI: 10.3389/fpls.2024.1389658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/19/2024] [Indexed: 06/01/2024]
Abstract
Environmental stressors disrupt secretory protein folding and proteostasis in the endoplasmic reticulum (ER), leading to ER stress. The unfolded protein response (UPR) senses ER stress and restores proteostasis by increasing the expression of ER-resident protein folding chaperones, such as protein disulfide isomerases (PDIs). In plants, the transmembrane ER stress sensor kinase, IRE1, activates the UPR by unconventionally splicing the mRNA encoding the bZIP60 transcription factor, triggering UPR gene transcription. The induced PDIs catalyze disulfide-based polypeptide folding to restore the folding capacity in the ER; however, the substrates with which PDIs interact are largely unknown. Here, we demonstrate that the Arabidopsis PDI-M subfamily member, PDI9, modulates the UPR through interaction with IRE1. This PDI9-IRE1 interaction was largely dependent on Cys63 in the first dithiol redox active domain of PDI9, and Cys233 and Cys107 in the ER lumenal domain of IRE1A and IRE1B, respectively. In vitro and in vivo, PDI9 coimmunoprecipitated with IRE1A and IRE1B. Moreover, the PDI9:RFP and Green Fluorescence Protein (GFP):IRE1 fusions exhibited strong interactions as measured by fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer (FLIM-FRET) when coexpressed in mesophyll protoplasts. The UPR-responsive PDI9 promoter:mCherry reporter and the UPR-dependent splicing of the bZIP60 intron from the mRNA of the 35S::bZIP60-intron:GFP reporter were both significantly induced in the pdi9 mutants, indicating a derepression and hyperactivation of UPR. The inductions of both reporters were substantially attenuated in the ire1a-ire1b mutant. We propose a model in which PDI9 modulates the UPR through two competing activities: secretory protein folding and via interaction with IRE1 to maintain proteostasis in plants.
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Affiliation(s)
| | | | | | | | - David A. Christopher
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, United States
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7
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Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
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Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
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8
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [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: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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Ouyang M, Xing Y, Zhang S, Li L, Pan Y, Deng L. Development of FRET Biosensor to Characterize CSK Subcellular Regulation. BIOSENSORS 2024; 14:206. [PMID: 38667199 PMCID: PMC11048185 DOI: 10.3390/bios14040206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
C-terminal Src kinase (CSK) is the major inhibitory kinase for Src family kinases (SFKs) through the phosphorylation of their C-tail tyrosine sites, and it regulates various types of cellular activity in association with SFK function. As a cytoplasmic protein, CSK needs be recruited to the plasma membrane to regulate SFKs' activity. The regulatory mechanism behind CSK activity and its subcellular localization remains largely unclear. In this work, we developed a genetically encoded biosensor based on fluorescence resonance energy transfer (FRET) to visualize the CSK activity in live cells. The biosensor, with an optimized substrate peptide, confirmed the crucial Arg107 site in the CSK SH2 domain and displayed sensitivity and specificity to CSK activity, while showing minor responses to co-transfected Src and Fyn. FRET measurements showed that CSK had a relatively mild level of kinase activity in comparison to Src and Fyn in rat airway smooth muscle cells. The biosensor tagged with different submembrane-targeting signals detected CSK activity at both non-lipid raft and lipid raft microregions, while it showed a higher FRET level at non-lipid ones. Co-transfected receptor-type protein tyrosine phosphatase alpha (PTPα) had an inhibitory effect on the CSK FRET response. The biosensor did not detect obvious changes in CSK activity between metastatic cancer cells and normal ones. In conclusion, a novel FRET biosensor was generated to monitor CSK activity and demonstrated CSK activity existing in both non-lipid and lipid raft membrane microregions, being more present at non-lipid ones.
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Affiliation(s)
- Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China; (Y.X.); (S.Z.); (L.L.); (Y.P.)
| | - Yujie Xing
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China; (Y.X.); (S.Z.); (L.L.); (Y.P.)
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Shumin Zhang
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China; (Y.X.); (S.Z.); (L.L.); (Y.P.)
| | - Liting Li
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China; (Y.X.); (S.Z.); (L.L.); (Y.P.)
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Yan Pan
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China; (Y.X.); (S.Z.); (L.L.); (Y.P.)
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China; (Y.X.); (S.Z.); (L.L.); (Y.P.)
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10
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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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11
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Damayanti NP, Cordova RA, Rupert C, Delle Fontane I, Shen L, Orsi S, Klunk AJ, Linehan WM, Staschke KA, Hollenhorst PC, Heppner DE, Pili R. TFE3-Splicing Factor Fusions Represent Functional Drivers and Druggable Targets in Translocation Renal Cell Carcinoma. Cancer Res 2024; 84:1286-1302. [PMID: 38266162 DOI: 10.1158/0008-5472.can-23-1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
TFE3 is a member of the basic helix-loop-helix leucine zipper MiT transcription factor family, and its chimeric proteins are associated with translocation renal cell carcinoma (tRCC). Despite the variety of gene fusions, most TFE3 fusion partner genes are related to spliceosome machinery. Dissecting the function of TFE3 fused to spliceosome machinery factors (TFE3-SF) could direct the development of effective therapies for this lethal disease, which is refractory to standard treatments for kidney cancer. Here, by using a combination of in silico structure prediction, transcriptome profiling, molecular characterization, and high-throughput high-content screening (HTHCS), we interrogated a number of oncogenic mechanisms of TFE3-SF fusions. TFE3-SF fusions drove the transformation of kidney cells and promoted distinct oncogenic phenotypes in a fusion partner-dependent manner, differentially altering the transcriptome and RNA splicing landscape and activating different oncogenic pathways. Inhibiting TFE3-SF dimerization reversed its oncogenic activity and represented a potential target for therapeutic intervention. Screening the FDA-approved drugs library LOPAC and a small-molecule library (Microsource) using HTHCS combined with FRET technology identified compounds that inhibit TFE3-SF dimerization. Hit compounds were validated in 2D and 3D patient-derived xenograft models expressing TFE3-SF. The antihistamine terfenadine decreased cell proliferation and reduced in vivo tumor growth of tRCC. Overall, these results unmask therapeutic strategies to target TFE3-SF dimerization for treating patients with tRCC. SIGNIFICANCE TFE3-splicing factor fusions possess both transcription and splicing factor functions that remodel the transcriptome and spliceosome and can be targeted with dimerization inhibitors to suppress the growth of translocation renal cell carcinoma.
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Affiliation(s)
- Nur P Damayanti
- Genitourinary Program, Division of Hematology & Oncology, Indiana University, Indianapolis, Indiana
- Department of Neurosurgery, Division of Neuro-Oncology, Indiana University, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Ricardo A Cordova
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - Christopher Rupert
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Ilaria Delle Fontane
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Li Shen
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Sabrina Orsi
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Angela J Klunk
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - W Marston Linehan
- Urological Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Kirk A Staschke
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - Peter C Hollenhorst
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - David E Heppner
- Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Roberto Pili
- Genitourinary Program, Division of Hematology & Oncology, Indiana University, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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12
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Fasano G, Petrini S, Bonavolontà V, Paradisi G, Pedalino C, Tartaglia M, Lauri A. Assessment of the FRET-based Teen sensor to monitor ERK activation changes preceding morphological defects in a RASopathy zebrafish model and phenotypic rescue by MEK inhibitor. Mol Med 2024; 30:47. [PMID: 38594640 PMCID: PMC11005195 DOI: 10.1186/s10020-024-00807-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND RASopathies are genetic syndromes affecting development and having variable cancer predisposition. These disorders are clinically related and are caused by germline mutations affecting key players and regulators of the RAS-MAPK signaling pathway generally leading to an upregulated ERK activity. Gain-of-function (GOF) mutations in PTPN11, encoding SHP2, a cytosolic protein tyrosine phosphatase positively controlling RAS function, underlie approximately 50% of Noonan syndromes (NS), the most common RASopathy. A different class of these activating mutations occurs as somatic events in childhood leukemias. METHOD Here, we evaluated the application of a FRET-based zebrafish ERK reporter, Teen, and used quantitative FRET protocols to monitor non-physiological RASopathy-associated changes in ERK activation. In a multi-level experimental workflow, we tested the suitability of the Teen reporter to detect pan-embryo ERK activity correlates of morphometric alterations driven by the NS-causing Shp2D61G allele. RESULTS Spectral unmixing- and acceptor photobleaching (AB)-FRET analyses captured pathological ERK activity preceding the manifestation of quantifiable body axes defects, a morphological pillar used to test the strength of SHP2 GoF mutations. Last, the work shows that by multi-modal FRET analysis, we can quantitatively trace back the modulation of ERK phosphorylation obtained by low-dose MEK inhibitor treatment to early development, before the onset of morphological defects. CONCLUSION This work proves the usefulness of FRET imaging protocols on both live and fixed Teen ERK reporter fish to readily monitor and quantify pharmacologically- and genetically-induced ERK activity modulations in early embryos, representing a useful tool in pre-clinical applications targeting RAS-MAPK signaling.
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Affiliation(s)
- Giulia Fasano
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Stefania Petrini
- Microscopy facility, Research laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Valeria Bonavolontà
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Graziamaria Paradisi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
- Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, 01100, Italy
| | - Catia Pedalino
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy.
| | - Antonella Lauri
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146, Italy.
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13
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Aubel M, Buchel F, Heames B, Jones A, Honc O, Bornberg-Bauer E, Hlouchova K. High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential. Genome Biol Evol 2024; 16:evae069. [PMID: 38597156 PMCID: PMC11024478 DOI: 10.1093/gbe/evae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024] Open
Abstract
De novo genes emerge from previously noncoding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Förster resonance energy transfer combined with Fluorescence-activated cell sorting, we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. We find that compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared with young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.
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Affiliation(s)
- Margaux Aubel
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Filip Buchel
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Brennen Heames
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Alun Jones
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Ondrej Honc
- Imaging Methods Core Facility, BIOCEV, Prague, Czech Republic
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
- Department of Protein Evolution, Max Planck-Institute for Biology Tuebingen, Tuebingen, Germany
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
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14
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Melle C, Hoffmann B, Wiesenburg A, Biskup C. FLIM-FRET-based analysis of S100A11/annexin interactions in living cells. FEBS Open Bio 2024; 14:626-642. [PMID: 38408765 PMCID: PMC10988696 DOI: 10.1002/2211-5463.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Proteins achieve their biological functions in cells by cooperation in protein complexes. In this study, we employed fluorescence lifetime imaging microscopy (FLIM)-based Förster resonance energy transfer (FRET) measurements to investigate protein complexes comprising S100A11 and different members of the annexin (ANX) family, such as ANXA1, ANXA2, ANXA4, ANXA5, and AnxA6, in living cells. Using an S100A11 mutant without the capacity for Ca2+ binding, we found that Ca2+ binding of S100A11 is important for distinct S100A11/ANXA2 complex formation; however, ANXA1-containing complexes were unaffected by this mutant. An increase in the intracellular calcium concentration induced calcium ionophores, which strengthened the ANXA2/S100A11 interaction. Furthermore, we were able to show that S100A11 also interacts with ANXA4 in living cells. The FLIM-FRET approach used here can serve as a tool to analyze interactions between S100A11 and distinct annexins under physiological conditions in living cells.
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Affiliation(s)
- Christian Melle
- Biomolecular Photonics Group, Jena University HospitalFriedrich Schiller University JenaGermany
| | - Birgit Hoffmann
- Biomolecular Photonics Group, Jena University HospitalFriedrich Schiller University JenaGermany
| | - Annett Wiesenburg
- Biomolecular Photonics Group, Jena University HospitalFriedrich Schiller University JenaGermany
| | - Christoph Biskup
- Biomolecular Photonics Group, Jena University HospitalFriedrich Schiller University JenaGermany
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15
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van der Horst J, Jepps TA. Proximity Labelling to Quantify Kv7.4 and Dynein Protein Interaction in Freshly Isolated Rat Vascular Smooth Muscle Cells. Bio Protoc 2024; 14:e4961. [PMID: 38841287 PMCID: PMC10958171 DOI: 10.21769/bioprotoc.4961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 06/07/2024] Open
Abstract
Understanding protein-protein interactions is crucial for unravelling subcellular protein distribution, contributing to our understanding of cellular organisation. Moreover, interaction studies can reveal insights into the mechanisms that cover protein trafficking within cells. Although various techniques such as Förster resonance energy transfer (FRET), co-immunoprecipitation, and fluorescence microscopy are commonly employed to detect protein interactions, their limitations have led to more advanced techniques such as the in situ proximity ligation assay (PLA) for spatial co-localisation analysis. The PLA technique, specifically employed in fixed cells and tissues, utilises species-specific secondary PLA probes linked to DNA oligonucleotides. When proteins are within 40 nm of each other, the DNA oligonucleotides on the probes interact, facilitating circular DNA formation through ligation. Rolling-circle amplification then produces DNA circles linked to the PLA probe. Fluorescently labelled oligonucleotides hybridise to the circles, generating detectable signals for precise co-localisation analysis. We employed PLA to examine the co-localisation of dynein with the Kv7.4 channel protein in isolated vascular smooth muscle cells from rat mesenteric arteries. This method enabled us to investigate whether Kv7.4 channels interact with dynein, thereby providing evidence of their retrograde transport by the microtubule network. Our findings illustrate that PLA is a valuable tool for studying potential novel protein interactions with dynein, and the quantifiable approach offers insights into whether these interactions are changed in disease.
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Affiliation(s)
- Jennifer van der Horst
- Vascular Biology Group, Department of Biomedical Sciences, University
of Copenhagen, Copenhagen, Denmark
| | - Thomas A. Jepps
- Vascular Biology Group, Department of Biomedical Sciences, University
of Copenhagen, Copenhagen, Denmark
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16
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Zhang F, Bischof H, Burgstaller S, Bourgeois BMR, Malli R, Madl T. Genetically encoded fluorescent sensor to monitor intracellular arginine methylation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 252:112867. [PMID: 38368636 DOI: 10.1016/j.jphotobiol.2024.112867] [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: 12/26/2023] [Revised: 02/03/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
Arginine methylation (ArgMet), as a post-translational modification, plays crucial roles in RNA processing, transcriptional regulation, signal transduction, DNA repair, apoptosis and liquid-liquid phase separation (LLPS). Since arginine methylation is associated with cancer pathogenesis and progression, protein arginine methyltransferases have gained interest as targets for anti-cancer therapy. Despite considerable process made to elucidate (patho)physiological mechanisms regulated by arginine methylation, there remains a lack of tools to visualize arginine methylation with high spatiotemporal resolution in live cells. To address this unmet need, we generated an ArgMet-sensitive genetically encoded, Förster resonance energy transfer-(FRET) based biosensor, called GEMS, capable of quantitative real-time monitoring of ArgMet dynamics. We optimized these biosensors by using different ArgMet-binding domains, arginine-glycine-rich regions and adjusting the linkers within the biosensors to improve their performance. Using a set of mammalian cell lines and modulators, we demonstrated the applicability of GEMS for monitoring changes in arginine methylation with single-cell and temporal resolution. The GEMS can facilitate the in vitro screening to find potential protein arginine methyltransferase inhibitors and will contribute to a better understanding of the regulation of ArgMet related to differentiation, development and disease.
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Affiliation(s)
- Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou 350122, China; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Helmut Bischof
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Sandra Burgstaller
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Benjamin M R Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Roland Malli
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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17
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Martinusen SG, Denard CA. Leveraging yeast sequestration to study and engineer posttranslational modification enzymes. Biotechnol Bioeng 2024; 121:903-914. [PMID: 38079116 PMCID: PMC11229454 DOI: 10.1002/bit.28621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024]
Abstract
Enzymes that catalyze posttranslational modifications (PTMs) of peptides and proteins (PTM-enzymes)-proteases, protein ligases, oxidoreductases, kinases, and other transferases-are foundational to our understanding of health and disease and empower applications in chemical biology, synthetic biology, and biomedicine. To fully harness the potential of PTM-enzymes, there is a critical need to decipher their enzymatic and biological mechanisms, develop molecules that can probe and modulate them, and endow them with improved and novel functions. These objectives are contingent upon implementation of high-throughput functional screens and selections that interrogate large sequence libraries to isolate desired PTM-enzyme properties. This review discusses the principles of Saccharomyces cerevisiae organelle sequestration to study and engineer PTM-enzymes. These include outer membrane sequestration, specifically methods that modify yeast surface display, and cytoplasmic sequestration based on enzyme-mediated transcription activation. Furthermore, we present a detailed discussion of yeast endoplasmic reticulum sequestration for the first time. Where appropriate, we highlight the major features and limitations of different systems, specifically how they can measure and control enzyme catalytic efficiencies. Taken together, yeast-based high-throughput sequestration approaches significantly lower the barrier to understanding how PTM-enzymes function and how to reprogram them.
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Affiliation(s)
- Samantha G Martinusen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
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18
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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19
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Rajan D, Muraleedharan A, Variyar A, Verma P, Pinhero F, Lakshmanna YA, Sabari Sankar T, Thomas KG. Single- and two-photon-induced Förster resonance energy transfer in InP-mCherry bioconjugates. J Chem Phys 2024; 160:044712. [PMID: 38294316 DOI: 10.1063/5.0186483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024] Open
Abstract
Indium phosphide (InP) quantum dots (QDs) have recently garnered considerable interest in the design of bioprobes due to their non-toxic nature and excellent optical properties. Several attempts for the conjunction of InP QDs with various entities such as organic dyes and dye-labeled proteins have been reported, while that with fluorescent proteins remains largely uncharted. This study reports the development of a Förster resonance energy transfer pair comprising glutathione-capped InP/GaP/ZnS QDs [InP(G)] and the fluorescent protein mCherry. Glutathione on InP(G) undergoes effective bioconjugation with mCherry consisting of a hexahistidine tag, and the nonradiative energy transfer is investigated using steady-state and time-resolved measurements. Selective one-photon excitation of InP(G) in the presence of mCherry shows a decay of the emission of the QDs and a concomitant growth of acceptor emission. Time-resolved investigations prove the nonradiative transfer of energy between InP(G) and mCherry. Furthermore, the scope of two-photon-induced energy transfer between InP(G) and mCherry is investigated by exciting the donor in the optical transparency range. The two-photon absorption is confirmed by the quadratic relationship between the emission intensity and the excitation power. In general, near-infrared excitation provides a path for effective light penetration into the tissues and reduces the photodamage of the sample. The two-photon-induced energy transfer in such assemblies could set the stage for a wide range of biological and optoelectronic applications in the foreseeable future.
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Affiliation(s)
- Devika Rajan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Ananthu Muraleedharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Anjali Variyar
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Preetika Verma
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Faina Pinhero
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Yapamanu Adithya Lakshmanna
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - T Sabari Sankar
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - K George Thomas
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
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20
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Bonilla PA, Shrestha R. FLIM-FRET Protein-Protein Interaction Assay. Methods Mol Biol 2024; 2797:261-269. [PMID: 38570466 DOI: 10.1007/978-1-0716-3822-4_19] [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: 04/05/2024]
Abstract
Fluorescence lifetime imaging performed under FRET conditions between two interacting molecules is a sensitive and robust way to quantify intermolecular interactions in cells. The fluorescence lifetime, an inherent property of the fluorophore, remains unaffected by factors such as concentration, laser intensity, and other photophysical artifacts. In the context of FLIM-FRET, the focus lies on measuring the fluorescence lifetime of the donor molecule, which diminishes upon interaction with a neighboring acceptor molecule. In this study, we present a step-by-step experimental protocol for applying FLIM-FRET to investigate protein-protein interactions involving various RAS isoforms and RAS effectors at the live cell's plasma membrane. By utilizing the FRET pair comprising enhanced green fluorescent protein (eGFP) and fluorescent mCherry, we demonstrate that the proximity and possible nanoclustering of eGFP-tagged KRAS4b G12D and mCherry-tagged KRAS4b WT led to a reduction in the donor eGFP's fluorescence lifetime. The donor lifetime of eGFP-tagged KRAS decreases even further when treated with a dimer-inducing small molecule, or in the presence of RAF proteins, suggesting a greater FRET efficiency, and thus less distance, between donor and acceptor.
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Affiliation(s)
- Pedro Andrade Bonilla
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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21
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Castillon GA, Phan S, Hu J, Boassa D, Adams SR, Ellisman MH. Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy. Sci Rep 2023; 13:21462. [PMID: 38052818 PMCID: PMC10697944 DOI: 10.1038/s41598-023-45413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023] Open
Abstract
The binding and interaction of proteins with nucleic acids such as DNA and RNA constitutes a fundamental biochemical and biophysical process in all living organisms. Identifying and visualizing such temporal interactions in cells is key to understanding their function. To image sites of these events in cells across scales, we developed a method, named PROMPT for PROximal Molecular Probe Transfer, which is applicable to both light and correlative electron microscopy. This method relies on the transfer of a bound photosensitizer from a protein known to associate with specific nucleic acid sequence, allowing the marking of the binding site on DNA or RNA in fixed cells. The method produces a fluorescent mark at the site of their interaction, that can be made electron dense and reimaged at high resolution in the electron microscope. As proof of principle, we labeled in situ the interaction sites between the histone H2B and nuclear DNA. As an example of application for specific RNA localizations we labeled different nuclear and nucleolar fractions of the protein Fibrillarin to mark and locate where it associates with RNAs, also using electron tomography. While the current PROMPT method is designed for microscopy, with minimal variations, it can be potentially expanded to analytical techniques.
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Affiliation(s)
- Guillaume A Castillon
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Junru Hu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniela Boassa
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, 92093, USA.
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22
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Shi X, Lingerak R, Herting CJ, Ge Y, Kim S, Toth P, Wang W, Brown BP, Meiler J, Sossey-Alaoui K, Buck M, Himanen J, Hambardzumyan D, Nikolov DB, Smith AW, Wang B. Time-resolved live-cell spectroscopy reveals EphA2 multimeric assembly. Science 2023; 382:1042-1050. [PMID: 37972196 PMCID: PMC11114627 DOI: 10.1126/science.adg5314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Ephrin type-A receptor 2 (EphA2) is a receptor tyrosine kinase that initiates both ligand-dependent tumor-suppressive and ligand-independent oncogenic signaling. We used time-resolved, live-cell fluorescence spectroscopy to show that the ligand-free EphA2 assembles into multimers driven by two types of intermolecular interactions in the ectodomain. The first type entails extended symmetric interactions required for ligand-induced receptor clustering and tumor-suppressive signaling that inhibits activity of the oncogenic extracellular signal-regulated kinase (ERK) and protein kinase B (AKT) protein kinases and suppresses cell migration. The second type is an asymmetric interaction between the amino terminus and the membrane proximal domain of the neighboring receptors, which supports oncogenic signaling and promotes migration in vitro and tumor invasiveness in vivo. Our results identify the molecular interactions that drive the formation of the EphA2 multimeric signaling clusters and reveal the pivotal role of EphA2 assembly in dictating its opposing functions in oncogenesis.
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Affiliation(s)
- Xiaojun Shi
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ryan Lingerak
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cameron J. Herting
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA 30322, USA
| | - Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Soyeon Kim
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Paul Toth
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Wei Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Benjamin P. Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Khalid Sossey-Alaoui
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Juha Himanen
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dolores Hambardzumyan
- Departments Oncological Sciences and Neurosurgery, Tisch Cancer Institute, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Adam W. Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Bingcheng Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
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23
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Sikora H, Gruba N, Wysocka M, Piwkowska A, Lesner A. Optimization of fluorescent substrates for ADAM17 and their utility in the detection of diabetes. Anal Biochem 2023; 681:115337. [PMID: 37783443 DOI: 10.1016/j.ab.2023.115337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
ADAM17 (a disintegrin and metalloproteinase 17) is a sheddase that releases various types of membrane-associated proteins, including adhesive molecules, cytokines and their receptors, and inflammatory mediators. Evidence suggests that the enzyme is involved in the proteolytic cleavage of antiaging transmembrane protein Klotho (KL). What is more, reduced serum and urinary KL levels are observed in the early stages of chronic kidney disease. This study aimed to optimise the ADAM17 specific and selective fluorescent substrates. Then, the obtained substrate was used to detect the enzyme in urine samples of patients diagnosed with diabetes. It turned out that in all cases we were able to detect proteolytic activity, which was the opposite of the healthy samples.
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Affiliation(s)
- Honorata Sikora
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Natalia Gruba
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, PL, 80-308, Gdańsk, Poland.
| | - Magdalena Wysocka
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Agnieszka Piwkowska
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute Polish Academy of Sciences, Wita Stwosza 63, 80-308, Gdansk, Poland; Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Adam Lesner
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, PL, 80-308, Gdańsk, Poland
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24
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Chen Y, Pang S, Li J, Lu Y, Gao C, Xiao Y, Chen M, Wang M, Ren X. Genetically encoded protein sensors for metal ion detection in biological systems: a review and bibliometric analysis. Analyst 2023; 148:5564-5581. [PMID: 37872814 DOI: 10.1039/d3an01412f] [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: 10/25/2023]
Abstract
Metal ions are indispensable elements in living organisms and are associated with regulating various biological processes. An imbalance in metal ion content can lead to disorders in normal physiological functions of the human body and cause various diseases. Genetically encoded fluorescent protein sensors have the advantages of low biotoxicity, high specificity, and a long imaging time in vivo and have become a powerful tool to visualize or quantify the concentration level of biomolecules in vivo and in vitro, temporal and spatial distribution, and life activity process. This review analyzes the development status and current research hotspots in the field of genetically encoded fluorescent protein sensors by bibliometric analysis. Based on the results of bibliometric analysis, the research progress of genetically encoded fluorescent protein sensors for metal ion detection is reviewed, and the construction strategies, physicochemical properties, and applications of such sensors in biological imaging are summarized.
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Affiliation(s)
- Yuxueyuan Chen
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuChao Pang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Jingya Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yun Lu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chenxia Gao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanyu Xiao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Meiling Chen
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Meng Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin 301617, China
| | - Xiaoliang Ren
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
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25
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Cheah LC, Liu L, Plan MR, Peng B, Lu Z, Schenk G, Vickers CE, Sainsbury F. Product Profiles of Promiscuous Enzymes Can be Altered by Controlling In Vivo Spatial Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303415. [PMID: 37750486 PMCID: PMC10646250 DOI: 10.1002/advs.202303415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Enzyme spatial organization is an evolved mechanism for facilitating multi-step biocatalysis and can play an important role in the regulation of promiscuous enzymes. The latter function suggests that artificial spatial organization can be an untapped avenue for controlling the specificity of bioengineered metabolic pathways. A promiscuous terpene synthase (nerolidol synthase) is co-localized and spatially organized with the preceding enzyme (farnesyl diphosphate synthase) in a heterologous production pathway, via translational protein fusion and/or co-encapsulation in a self-assembling protein cage. Spatial organization enhances nerolidol production by ≈11- to ≈62-fold relative to unorganized enzymes. More interestingly, striking differences in the ratio of end products (nerolidol and linalool) are observed with each spatial organization approach. This demonstrates that artificial spatial organization approaches can be harnessed to modulate the product profiles of promiscuous enzymes in engineered pathways in vivo. This extends the application of spatial organization beyond situations where multiple enzymes compete for a single substrate to cases where there is competition among multiple substrates for a single enzyme.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Present address:
Australian Centre for Disease Preparedness5 Portarlington RdEast GeelongVIC3219Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Manuel R. Plan
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
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26
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Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023; 480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
Abstract
As cell signaling research has advanced, it has become clearer that signal transduction has complex spatiotemporal regulation that goes beyond foundational linear transduction models. Several technologies have enabled these discoveries, including fluorescent biosensors designed to report live biochemical signaling events. As genetically encoded and live-cell compatible tools, fluorescent biosensors are well suited to address diverse cell signaling questions across different spatial scales of regulation. In this review, methods of examining spatial signaling regulation and the design of fluorescent biosensors are introduced. Then, recent biosensor developments that illuminate the importance of spatial regulation in cell signaling are highlighted at several scales, including membranes and organelles, molecular assemblies, and cell/tissue heterogeneity. In closing, perspectives on how fluorescent biosensors will continue enhancing cell signaling research are discussed.
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Affiliation(s)
- Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, U.S.A
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27
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Jeong HJ. Quenchbodies That Enable One-Pot Detection of Antigens: A Structural Perspective. Bioengineering (Basel) 2023; 10:1262. [PMID: 38002387 PMCID: PMC10669387 DOI: 10.3390/bioengineering10111262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Quenchbody (Q-body) is a unique, reagentless, fluorescent antibody whose fluorescent intensity increases in an antigen-concentration-dependent manner. Q-body-based homogeneous immunoassay is superior to conventional immunoassays as it does not require multiple immobilization, reaction, and washing steps. In fact, simply mixing the Q-body and the sample containing the antigen enables the detection of the target antigen. To date, various Q-bodies have been developed to detect biomarkers of interest, including haptens, peptides, proteins, and cells. This review sought to describe the principle of Q-body-based immunoassay and the use of Q-body for various immunoassays. In particular, the Q-bodies were classified from a structural perspective to provide useful information for designing Q-bodies with an appropriate objective.
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Affiliation(s)
- Hee-Jin Jeong
- Department of Biological and Chemical Engineering, Hongik University, Sejong-si 30016, Republic of Korea
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28
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Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
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Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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29
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Castillon GA, Phan S, Hu J, Boassa D, Adams SR, Ellisman MH. Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542936. [PMID: 37808832 PMCID: PMC10557592 DOI: 10.1101/2023.05.30.542936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The binding and interaction of proteins with nucleic acids such as DNA and RNA constitutes a fundamental biochemical and biophysical process in all living organisms. Identifying and visualizing such temporal interactions in cells is key to understanding their function. To image sites of these events in cells across scales, we developed a method, named PROMPT for PROximal Molecular Probe Transfer, which is applicable to both light and correlative electron microscopy. This method relies on the transfer of a bound photosensitizer from a protein known to associate with specific nucleic acid sequence, allowing the marking of the binding site on DNA or RNA in fixed cells. The method produces a fluorescent mark at the site of their interaction, that can be made electron dense and reimaged at high resolution in the electron microscope. As proof of principle, we labeled in situ the interaction sites between the histone H2B and nuclear DNA. As an example of application for specific RNA localizations we labeled different nuclear and nucleolar fractions of the protein Fibrillarin to mark and locate where it associates with RNAs, also using electron tomography. While the current PROMPT method is designed for microscopy, with minimal variations, it can be potentially expanded to analytical techniques.
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30
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Singh Chauhan S, Mohan Murari B. Fluorescence Spectroscopic Studies to Evaluate Binding Interaction between Hoechst 33258 and Bilirubin. J Fluoresc 2023:10.1007/s10895-023-03440-8. [PMID: 37728846 DOI: 10.1007/s10895-023-03440-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
A detailed spectroscopic study (fluorescence, absorption, and lifetime) was conducted to gain insight into the nature of the binding interaction between fluorophore Hoechst33258 (H258) and jaundice marker Bilirubin (Br). The fluorescence emission of the H258 (Ex/Em = 340-502nm) showed a conc. dependent quenching in the presence of Br (1.25[Formula: see text]M to 10[Formula: see text]M). The Stern-Volmer constant demonstrated an upward curve depicting the occurrence of both static and dynamic quenching with an acquired value of K[Formula: see text] = 3.1x 10[Formula: see text] M[Formula: see text] and biomolecular quenching rate constant K[Formula: see text] = 8.6 x 10[Formula: see text] M[Formula: see text]S[Formula: see text]. The static quenching was evaluated using the sphere of action model and a sphere radius of 0.3nm indicated the presence of a static component in the quenching. The FRET analysis with overlap integral (J) = 1.4x10[Formula: see text] M[Formula: see text]cm[Formula: see text]nm[Formula: see text] and Foster Radius(R[Formula: see text]) = 26.82 Å with 59% efficiency suggested occurrence of dynamic quenching. Further studies with the time-resolved fluorescence also indicated the presence of dynamic quenching. The lifetime values of H258 reduced from 3.9ns to 0.5ns. Molecular docking studies further support both static and dynamic components in quenching. A non-covalent interaction of H258 with Br in the presence of HSA is predominantly characterized by H-bonding with residues Lys, Asn, Glu, Gln, and Br. The H258 and Br interaction was within the distance of 3.04 Å, which is in coherence with the sphere of action model (0.3nm) and Van-der-Waals along with hydrophobic interactions, which suggested both static and dynamic quenching. Thus, H258 can serve as an efficient fluorophore to monitor binding interactions and can be further exploited as a suitable probe for investigating conformational changes and detection of Br in subsequent studies.
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Affiliation(s)
- Srishti Singh Chauhan
- Department of Sensor and Biomedical Technology, School of Electronics Engineering, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Bhaskar Mohan Murari
- Department of Sensor and Biomedical Technology, School of Electronics Engineering, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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31
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Wu Y, Lewis W, Wai JL, Xiong M, Zheng J, Yang Z, Gordon C, Lu Y, New SY, Zhang XB, Lu Y. Ratiometric Detection of Zn 2+ Using DNAzyme-Based Bioluminescence Resonance Energy Transfer Sensors. CHEMISTRY (BASEL, SWITZERLAND) 2023; 5:1745-1759. [PMID: 38371491 PMCID: PMC10874629 DOI: 10.3390/chemistry5030119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer (BRET)-based protein or small molecule sensors have been developed; however, most of them are not highly selective nor generalizable to different metal ions. Taking advantage of the high selectivity and generalizability of DNAzymes, we report herein DNAzyme-based ratiometric sensors for Zn2+ based on BRET. The 8-17 DNAzyme was labeled with luciferase and Cy3. The proximity between luciferase and Cy3 permiQed BRET when coelenterazine, the substrate for luciferase, was introduced. Adding samples containing Zn2+ resulted in a cleavage of the substrate strand, causing dehybridization of the DNAzyme construct, thus increasing the distance between Cy3 and luciferase and changing the BRET signals. Using these sensors, we detected Zn2+ in serum samples and achieved Zn2+ detection with a smartphone camera. Moreover, since the BRET pair is not the component that determines the selectivity of the sensors, this sensing platform has the potential to be adapted for the detection of other metal ions with other metal-dependent DNAzymes.
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Affiliation(s)
- Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Whitney Lewis
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jing Luen Wai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- School of Pharmacy, Faculty of Science and Engineering, University of No0ingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Mengyi Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jiao Zheng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chloe Gordon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ying Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Siu Yee New
- School of Pharmacy, Faculty of Science and Engineering, University of No0ingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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McCarthy M, Dodd WB, Lu X, Pritko DJ, Patel ND, Haskell CV, Sanabria H, Blenner MA, Birtwistle MR. Theory for High-Throughput Genetic Interaction Screening. ACS Synth Biol 2023; 12:2290-2300. [PMID: 37463472 PMCID: PMC10443530 DOI: 10.1021/acssynbio.2c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 07/20/2023]
Abstract
Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼105 spectrally unique, genetically encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
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Affiliation(s)
- Madeline
E. McCarthy
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Xiaoming Lu
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Daniel J. Pritko
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Nishi D. Patel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Charlotte V. Haskell
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Hugo Sanabria
- Department
of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, United States
| | - Mark A. Blenner
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29631, United States
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33
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Loder S, Patel N, Morgani S, Sambon M, Leucht P, Levi B. Genetic models for lineage tracing in musculoskeletal development, injury, and healing. Bone 2023; 173:116777. [PMID: 37156345 PMCID: PMC10860167 DOI: 10.1016/j.bone.2023.116777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
Musculoskeletal development and later post-natal homeostasis are highly dynamic processes, marked by rapid structural and functional changes across very short periods of time. Adult anatomy and physiology are derived from pre-existing cellular and biochemical states. Consequently, these early developmental states guide and predict the future of the system as a whole. Tools have been developed to mark, trace, and follow specific cells and their progeny either from one developmental state to the next or between circumstances of health and disease. There are now many such technologies alongside a library of molecular markers which may be utilized in conjunction to allow for precise development of unique cell 'lineages'. In this review, we first describe the development of the musculoskeletal system beginning as an embryonic germ layer and at each of the key developmental stages that follow. We then discuss these structures in the context of adult tissues during homeostasis, injury, and repair. Special focus is given in each of these sections to the key genes involved which may serve as markers of lineage or later in post-natal tissues. We then finish with a technical assessment of lineage tracing and the techniques and technologies currently used to mark cells, tissues, and structures within the musculoskeletal system.
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Affiliation(s)
- Shawn Loder
- Department of Plastic Surgery, University of Pittsburgh, Scaife Hall, Suite 6B, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Nicole Patel
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | - Benjamin Levi
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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34
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Zhao L, Song Q, Mai W, Deng M, Lei Y, Chen L, Kong W, Zhang L, Zhang L, Li Y, Ye H, Qin Y, Zhang T, Hu Y, Ji T, Wei W. Engineering highly efficient NIR-II FRET platform for Background-Free homogeneous detection of SARS-CoV-2 neutralizing antibodies in whole blood. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2023; 468:143616. [PMID: 37251501 PMCID: PMC10195770 DOI: 10.1016/j.cej.2023.143616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
Förster or fluorescence resonance energy transfer (FRET) enables to probe biomolecular interactions, thus playing a vital role in bioassays. However, conventional FRET platforms suffer from limited sensitivity due to the low FRET efficiency and poor anti-interference of existing FRET pairs. Here we report a NIR-II (1000-1700 nm) FRET platform with extremely high FRET efficiency and exceptional anti-interference capability. This NIR-II FRET platform is established based on a pair of lanthanides downshifting nanoparticles (DSNPs) by employing Nd3+ doped DSNPs as an energy donor and Yb3+ doped DSNPs as an energy acceptor. The maximum FRET efficiency of this well-engineered NIR-II FRET platform reaches up to 92.2%, which is much higher than most commonly used ones. Owing to the all-NIR advantage (λex = 808 nm, λem = 1064 nm), this highly efficient NIR-II FRET platform exhibits extraordinary anti-interference in whole blood, and thus enabling background-free homogeneous detection of SARS-CoV-2 neutralizing antibodies in clinical whole blood sample with high sensitivity (limit of detection = 0.5 μg/mL) and specificity. This work opens up new opportunities for realizing highly sensitive detection of various biomarkers in biological samples with severe background interference.
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Affiliation(s)
- Lei Zhao
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Qingwei Song
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Weikang Mai
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Deng
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Lei
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lu Chen
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiya Kong
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lei Zhang
- Kidney Transplant Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lin Zhang
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yantao Li
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Huiru Ye
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yiru Qin
- Guangdong Provincial Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China
| | - Tao Zhang
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yongjun Hu
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Tianxing Ji
- Clinical Laboratory Medicine Department, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wei
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
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35
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Lin Y, Tao X, Gao S, Li N, Dai Z. Highly sensitive and stable fluorescent aptasensor based on an exonuclease III-assisted amplification strategy for ATP detection. Anal Biochem 2023:115210. [PMID: 37329966 DOI: 10.1016/j.ab.2023.115210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023]
Abstract
Fluctuations in intracellular adenosine triphosphate (ATP) concentration are closely associated with some cancer diseases. Thus, it is a worthwhile undertaking to predict sickness by monitoring changes in ATP levels. However, the detection limits of current fluorescent aptamer sensors for ATP detection are in the range of nmol L-1 to μmol L-1. It has become crucial to employ amplification strategies to increase the sensitivity of fluorescent aptamer sensors. In the current paper, a duplex hybrid aptamer probe was developed based on exonuclease III (Exo III)-catalyzed target recycling amplification for ATP detection. The target ATP forced the duplex probe configuration to change into a molecular beacon that can be hydrolyzed with Exo III to achieve the target ATP cycling to amplify the fluorescence signal. Significantly, many researchers ignore that FAM is a pH-sensitive fluorophore, leading to the fluorescence instability of FAM-modified probes in different pH buffers. The negatively charged ions on the surface of AuNPs were replaced by new ligands bis(p-sulfonatophenyl)phenylphosphine dihydrate dipotassium salt (BSPP) to improve the drawback of FAM instability in alkaline solutions in this work. The aptamer probe was designed to eliminate the interference of other similar small molecules, showing specific selectivity and providing ultra-sensitive detection of ATP with detection limits (3σ) as low as 3.35 nM. Such detection limit exhibited about 4-500-fold better than that of the other amplification strategies for ATP detection. Thus, a relatively general high sensitivity detection system can be established according to the wide target adaptability of aptamers, which can form specific binding with different types of targets.
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Affiliation(s)
- Yushuang Lin
- School of Textile Science and Engineering, Tiangong University, Tianjin, 300387, China
| | - Xuejiao Tao
- School of Textile Science and Engineering, Tiangong University, Tianjin, 300387, China
| | - Suhan Gao
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, China
| | - Nan Li
- School of Chemistry, Tiangong University, Tianjin, 300387, China.
| | - Zhao Dai
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, China.
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36
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Sheokand M, Ji Tiwari N, Misra R. Near-IR absorbing 1,1,4,4-tetracyanobutadiene-functionalized phenothiazine sulfones. Org Biomol Chem 2023; 21:3896-3905. [PMID: 37165921 DOI: 10.1039/d3ob00361b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Triphenylamine (TPA) substituted π-conjugated chromophores TPA1-TPA5 were designed and synthesized via Pd-catalysed Sonogashira cross-coupling followed by [2 + 2] cycloaddition-retroelectrocyclization (CA-RE) reactions. The effects of acceptor 1,1,4,4-tetracyanobutadiene (TCBD) and cyclohexa-2,5-diene-1,4-diylidene-expanded TCBD (DCNQ) units in the photophysical studies and the HOMO-LUMO energy levels of the phenothiazine sulfones TPA1-TPA5 were evaluated. The absorption spectra of chromophores TPA4 and TPA5 show a significant change due to the incorporation of DCNQ units, resulting in bathochromically shifted broad absorption in the NIR region. The photophysical studies revealed that DCNQ-based chromophores TPA4 and TPA5 have a better D-A interaction than the TCBD functionalized TPA2 and TPA3. Density functional theory calculations and electrochemical studies were performed to examine the molecular geometry and frontier energy levels of the sulfone-based chromophores. Systematic structural modification of the chromophore TPA1 modulated the electrochemical properties and successively tuned the energy gaps for TPA2-TPA5. The theoretically estimated HOMO-LUMO gaps for TPA1-TPA5 exhibit good agreement with the experimental data calculated from the electrochemical studies. The chromophore TPA1 exhibits solvatochromism and aggregation-induced emission (AIE) behavior owing to the emission in the solid state.
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Affiliation(s)
- Manju Sheokand
- Department of Chemistry, Indian Institute of Technology Indore, Indore-453552, India.
| | - Nikhil Ji Tiwari
- Department of Chemistry, Indian Institute of Technology Indore, Indore-453552, India.
| | - Rajneesh Misra
- Department of Chemistry, Indian Institute of Technology Indore, Indore-453552, India.
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37
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Kamino K, Kadakia N, Avgidis F, Liu ZX, Aoki K, Shimizu T, Emonet T. Optimal inference of molecular interaction dynamics in FRET microscopy. Proc Natl Acad Sci U S A 2023; 120:e2211807120. [PMID: 37014867 PMCID: PMC10104582 DOI: 10.1073/pnas.2211807120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/10/2023] [Indexed: 04/05/2023] Open
Abstract
Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible-a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on Bayesian filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.
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Affiliation(s)
- Keita Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Institute of Molecular Biology, Academia Sinica, Taipei115, Taiwan
- PRESTO, Japan Science and Technology Agency, Kawaguchi-shi, Saitama332-0012, Japan
| | - Nirag Kadakia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Swartz Foundation for Theoretical Neuroscience, Yale University, New Haven, CT06511
| | | | - Zhe-Xuan Liu
- Institute of Physics, National Yang Ming Chiao Tung University, Hsinchu30010, Taiwan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi240-0193, Japan
| | | | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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38
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Verma AK, Noumani A, Yadav AK, Solanki PR. FRET Based Biosensor: Principle Applications Recent Advances and Challenges. Diagnostics (Basel) 2023; 13:diagnostics13081375. [PMID: 37189476 DOI: 10.3390/diagnostics13081375] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
Förster resonance energy transfer (FRET)-based biosensors are being fabricated for specific detection of biomolecules or changes in the microenvironment. FRET is a non-radiative transfer of energy from an excited donor fluorophore molecule to a nearby acceptor fluorophore molecule. In a FRET-based biosensor, the donor and acceptor molecules are typically fluorescent proteins or fluorescent nanomaterials such as quantum dots (QDs) or small molecules that are engineered to be in close proximity to each other. When the biomolecule of interest is present, it can cause a change in the distance between the donor and acceptor, leading to a change in the efficiency of FRET and a corresponding change in the fluorescence intensity of the acceptor. This change in fluorescence can be used to detect and quantify the biomolecule of interest. FRET-based biosensors have a wide range of applications, including in the fields of biochemistry, cell biology, and drug discovery. This review article provides a substantial approach on the FRET-based biosensor, principle, applications such as point-of-need diagnosis, wearable, single molecular FRET (smFRET), hard water, ions, pH, tissue-based sensors, immunosensors, and aptasensor. Recent advances such as artificial intelligence (AI) and Internet of Things (IoT) are used for this type of sensor and challenges.
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Affiliation(s)
- Awadhesh Kumar Verma
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashab Noumani
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Amit K Yadav
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pratima R Solanki
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
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39
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Zhou Y, Centeno SP, Zhang K, Zheng L, Göstl R, Herrmann A. Fracture Detection in Bio-Glues with Fluorescent-Protein-Based Optical Force Probes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210052. [PMID: 36740969 DOI: 10.1002/adma.202210052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Glues are being used to bond, seal, and repair in industry and biomedicine. The improvement of gluing performance is hence important for the development of new glues with better and balanced property spaces, which in turn necessitates a mechanistic understanding of their mechanical failure. Optical force probes (OFPs) allow the observation of mechanical material damage in polymers from the macro- down to the microscale, yet have never been employed in glues. Here, the development of a series of ratiometric OFPs based on fluorescent-protein-dye and protein-protein conjugates and their incorporation into genetically engineered bio-glues is reported. The OFPs are designed to efficiently modulate Förster resonance energy transfer upon force application thereby reporting on force-induced molecular alterations independent of concentration and fluorescence intensity both spectrally and through their fluorescence lifetime. By fluorescence spectroscopy in solution and in the solid state and by fluorescence lifetime imaging microscopy, stress concentrations are visualized and adhesive and cohesive failure in the fracture zone is differentiated.
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Affiliation(s)
- Yu Zhou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Silvia P Centeno
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
| | - Kuan Zhang
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, China
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Lifei Zheng
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, China
| | - Robert Göstl
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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40
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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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41
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Sudewi S, Chabib L, Zulfajri M, Gedda G, Huang GG. Polyvinylpyrrolidone-passivated fluorescent iron oxide quantum dots for turn-off detection of tetracycline in biological fluids. J Food Drug Anal 2023; 31:177-193. [PMID: 37224556 PMCID: PMC10208663 DOI: 10.38212/2224-6614.3440] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/28/2022] [Indexed: 06/03/2024] Open
Abstract
Tetracycline is an antibiotic that has been prescribed for COVID-19 treatment, raising concerns about antibiotic resistance after long-term use. This study reported fluorescent polyvinylpyrrolidone-passivated iron oxide quantum dots (IO QDs) for detecting tetracycline in biological fluids for the first time. The as-prepared IO QDs have an average size of 2.84 nm and exist a good stability under different conditions. The IO QDs' tetracycline detection performance could be attributed to a combination of static quenching and inner filter effect. The IO QDs displayed high sensitivity and selectivity toward tetracycline and achieved a good linear relationship with the corresponding detection limit being 91.6 nM.
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Affiliation(s)
- Sri Sudewi
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 80708,
Taiwan
- Department of Pharmacy, Faculty of Mathematics and Natural Science, Universitas Sam Ratulangi, Manado, 95115,
Indonesia
| | - Lutfi Chabib
- Department of Pharmacy, Faculty of Mathematics and Science, Universitas Islam Indonesia, Yogyakarta, 55584,
Indonesia
| | - Muhammad Zulfajri
- Department of Chemistry Education, Universitas Serambi Mekkah, Banda Aceh, Aceh, 23245,
Indonesia
| | - Gangaraju Gedda
- Department of Chemistry, School of Engineering, Presidency University, Bangalore, 560064, Karnataka,
India
| | - Genin G. Huang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 80708,
Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 80708,
Taiwan
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, 80424,
Taiwan
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42
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Sorenson AE, Schaeffer PM. Real-Time Temperature Sensing Using a Ratiometric Dual Fluorescent Protein Biosensor. BIOSENSORS 2023; 13:338. [PMID: 36979550 PMCID: PMC10046200 DOI: 10.3390/bios13030338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Accurate temperature control within biological and chemical reaction samples and instrument calibration are essential to the diagnostic, pharmaceutical and chemical industries. This is particularly challenging for microlitre-scale reactions typically used in real-time PCR applications and differential scanning fluorometry. Here, we describe the development of a simple, inexpensive ratiometric dual fluorescent protein temperature biosensor (DFPTB). A combination of cycle three green fluorescent protein and a monomeric red fluorescent protein enabled the quantification of relative temperature changes and the identification of temperature discrepancies across a wide temperature range of 4-70 °C. The maximal sensitivity of 6.7% °C-1 and precision of 0.1 °C were achieved in a biologically relevant temperature range of 25-42 °C in standard phosphate-buffered saline conditions at a pH of 7.2. Good temperature sensitivity was achieved in a variety of biological buffers and pH ranging from 4.8 to 9.1. The DFPTB can be used in either purified or mixed bacteria-encapsulated formats, paving the way for in vitro and in vivo applications for topologically precise temperature measurements.
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43
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Luo W, Wang C, Min J, Luo H. Gold nanoclusters Cys-Au NCs as selective fluorescent probes for "on-off-on" detection of Fe 3+ and ascorbic acid. RSC Adv 2023; 13:7425-7431. [PMID: 36895769 PMCID: PMC9990083 DOI: 10.1039/d3ra00410d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Gold nanoclusters exhibit attractive properties owing to their excellent biocompatibility and strong photostability in the biomedical domain. In this research, cysteine-protected fluorescent gold nanoclusters (Cys-Au NCs) were synthesized via decomposing Au(i)-thiolate complexes for the detection of Fe3+ and ascorbic acid in a bidirectional "on-off-on" mode. Meanwhile, the detailed characterization confirmed that the mean particle size of the prepared fluorescent probe was 2.43 nm and showed a fluorescence quantum yield of 3.31%. In addition, our results indicate that the fluorescence probe for ferric ions exhibited a broad detection scope ranging from 0.1 to 2000 μM and excellent selectivity. The as-prepared Cys-Au NCs/Fe3+ was demonstrated to be an ultrasensitive and selective nanoprobe for the detection of ascorbic acid. This study indicated that the "on-off-on" fluorescent probes Cys-Au NCs held a promising application for the bidirectional detection of Fe3+ and ascorbic acid. Furthermore, our novel "on-off-on" fluorescent probes provided insight into the rational design of thiolate-protected gold nanoclusters for biochemical analysis of high selectivity and sensitivity.
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Affiliation(s)
- Wenjie Luo
- Department of Pharmacy, Xiangyang No.1 People's Hospital, Hubei University of Medicine Xiangyang 441000 China
| | - Changxu Wang
- Department of Pharmacy, Taihe Hospital, Hubei University of Medicine Shiyan 442000 China
| | - Jieshu Min
- Department of Pharmacy, Xiangyang No.1 People's Hospital, Hubei University of Medicine Xiangyang 441000 China
| | - Huiyu Luo
- Department of Anesthesiology, Xiangyang Key Laboratory of Movement Disorders, Xiangyang No.1 People's Hospital, Hubei University of Medicine Xiangyang 441000 China
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44
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Gohil K, Wu SY, Takahashi-Yamashiro K, Shen Y, Campbell RE. Biosensor Optimization Using a Förster Resonance Energy Transfer Pair Based on mScarlet Red Fluorescent Protein and an mScarlet-Derived Green Fluorescent Protein. ACS Sens 2023; 8:587-597. [PMID: 36693235 DOI: 10.1021/acssensors.2c01730] [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: 01/26/2023]
Abstract
Genetically encoded biosensors based on Förster resonance energy transfer (FRET) are indispensable tools for monitoring biochemical changes in cells. Green and red fluorescent protein-based FRET pairs offer advantages over the classically employed cyan and yellow fluorescent protein pairs, such as better spectral separation, lower phototoxicity, and less autofluorescence. Here, we describe the development of an mScarlet-derived green fluorescent protein (designated as mWatermelon) and its use as a FRET donor to the red fluorescent protein mScarlet-I as a FRET acceptor. We tested the functionality of this FRET pair by engineering biosensors for the detection of protease activity, Ca2+, and K+. Furthermore, we described a strategy to enhance the FRET efficiency of these biosensors by modulating the intramolecular association between mWatermelon and mScarlet-I.
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Affiliation(s)
- Khyati Gohil
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.,Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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45
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [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: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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47
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Investigating Plant Protein-Protein Interactions Using FRET-FLIM with a Focus on the Actin Cytoskeleton. Methods Mol Biol 2023; 2604:353-366. [PMID: 36773249 DOI: 10.1007/978-1-0716-2867-6_29] [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: 02/12/2023]
Abstract
The study of protein-protein interactions is fundamental to understanding how actin-dependent processes are controlled through the regulation of actin-binding proteins by their interactors. FRET-FLIM (Förster resonance energy transfer-fluorescence lifetime imaging microscopy) is a sensitive bioimaging method to detect protein-protein interactions in living cells through measurement of FRET, facilitated by the interactions of fluorophore-tagged fusion protein. As a sensitive and noninvasive method for the spatiotemporal visualization of dynamic protein-protein interactions, FRET-FLIM holds several advantages over other methods of protein interaction assays. FRET-FLIM has been widely employed to characterize many plant protein interactions, including interactions between actin-regulatory proteins and their binding partners. As we increasingly understand the plant actin cytoskeleton to coordinate a diverse number of complex functions, the study of actin-regulatory proteins and their interactors becomes increasingly technically challenging. Sophisticated and sensitive in vivo methods such as FRET-FLIM are likely to be crucial to the study of protein-protein interactions as more complex and challenging hypotheses are addressed.
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48
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Zhang M, Sun Y. DNA-based customized functional modules for signal transformation. Front Chem 2023; 11:1140022. [PMID: 36864900 PMCID: PMC9971431 DOI: 10.3389/fchem.2023.1140022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Information on the temporal and spatial scale of cellular molecules in biological systems is crucial for estimating life processes and may be conducive to an improved understanding of disease progression. This intracellular and extracellular information is often difficult to obtain at the same time due to the limitations of accessibility and sensing throughput. DNA is an excellent material for in vivo and in vitro applications, and can be used to build functional modules that can transform bio-information (input) into ATCG sequence information (output). Due to their small volume and highly amenable programming, DNA-based functional modules provide an opportunity to monitor a range of information, from transient molecular events to dynamic biological processes. Over the past two decades, with the advent of customized strategies, a series of functional modules based on DNA networks have been designed to gather different information about molecules, including the identity, concentration, order, duration, location, and potential interactions; the action of these modules are based on the principle of kinetics or thermodynamics. This paper summarizes the available DNA-based functional modules that can be used for biomolecular signal sensing and transformation, reviews the available designs and applications of these modules, and assesses current challenges and prospects.
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Affiliation(s)
- Mingzhi Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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49
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Xia S, Vila Ellis L, Winkley K, Menden H, Mabry SM, Venkatraman A, Louiselle D, Gibson M, Grundberg E, Chen J, Sampath V. Neonatal hyperoxia induces activated pulmonary cellular states and sex-dependent transcriptomic changes in a model of experimental bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol 2023; 324:L123-L140. [PMID: 36537711 PMCID: PMC9902224 DOI: 10.1152/ajplung.00252.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Hyperoxia disrupts lung development in mice and causes bronchopulmonary dysplasia (BPD) in neonates. To investigate sex-dependent molecular and cellular programming involved in hyperoxia, we surveyed the mouse lung using single cell RNA sequencing (scRNA-seq), and validated our findings in human neonatal lung cells in vitro. Hyperoxia-induced inflammation in alveolar type (AT) 2 cells gave rise to damage-associated transient progenitors (DATPs). It also induced a new subpopulation of AT1 cells with reduced expression of growth factors normally secreted by AT1 cells, but increased mitochondrial gene expression. Female alveolar epithelial cells had less EMT and pulmonary fibrosis signaling in hyperoxia. In the endothelium, expansion of Car4+ EC (Cap2) was seen in hyperoxia along with an emergent subpopulation of Cap2 with repressed VEGF signaling. This regenerative response was increased in females exposed to hyperoxia. Mesenchymal cells had inflammatory signatures in hyperoxia, with a new distal interstitial fibroblast subcluster characterized by repressed lipid biosynthesis and a transcriptomic signature resembling myofibroblasts. Hyperoxia-induced gene expression signatures in human neonatal fibroblasts and alveolar epithelial cells in vitro resembled mouse scRNA-seq data. These findings suggest that neonatal exposure to hyperoxia programs distinct sex-specific stem cell progenitor and cellular reparative responses that underpin lung remodeling in BPD.
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Affiliation(s)
- Sheng Xia
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Lisandra Vila Ellis
- Department of Pulmonary Medicine, University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Konner Winkley
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
| | - Heather Menden
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Sherry M Mabry
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Aparna Venkatraman
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Daniel Louiselle
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri
- Children's Mercy Research Institute, Kansas City, Missouri
| | - Jichao Chen
- Department of Pulmonary Medicine, University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Venkatesh Sampath
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
- Children's Mercy Research Institute, Kansas City, Missouri
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50
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Alam SR, Mahadevan MS, Periasamy A. Detecting RNA-Protein Interactions With EGFP-Cy3 FRET by Acceptor Photobleaching. Curr Protoc 2023; 3:e689. [PMID: 36821783 DOI: 10.1002/cpz1.689] [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
Förster Resonance Energy Transfer (FRET) is a great tool for cell biologists to investigate molecular interactions in live specimens. FRET is a distance-dependent phenomenon which can detect molecular interactions at distances between 1-10 nm. Several FRET approaches are reported in the literature for live and fixed cells to study protein-protein interactions; this protocol provides details of acceptor photobleaching as a FRET method to study RNA-Protein interactions. Cy3-labeled RNA foci (FRET acceptors) are photobleached at the intra-cellular site of interest (the nuclei) and the intensity of the EGFP-tagged proteins (FRET donors) at that same site are measured pre- and post- photobleaching. In principle, FRET is detected if the intensity of EGFP increases after photobleaching of Cy3. This protocol describes necessary steps and appropriate controls to conduct FRET measurements by the acceptor photobleaching method. Successful applications of this protocol will provide data to support the conclusion that EGFP-labeled proteins directly interact with Cy3-labeled RNA at the site of photobleaching. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: FRET in fixed cells Alternate Protocol: FRET in live cells.
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Affiliation(s)
- Shagufta Rehman Alam
- W. M. Keck Center for Cellular Imaging, University of Virginia, Charlottesville, Virginia
| | - Mani S Mahadevan
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Ammasi Periasamy
- W. M. Keck Center for Cellular Imaging, University of Virginia, Charlottesville, Virginia.,Departments of Biology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia
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