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Rahman MS, Shindo Y, Oka K, Ikeda W, Suzuki M. Live Cell Monitoring of Separase Activity, a Key Enzymatic Reaction for Chromosome Segregation, with Chimeric FRET-Based Molecular Sensor upon Cell Cycle Progression. BIOSENSORS 2024; 14:192. [PMID: 38667185 PMCID: PMC11048197 DOI: 10.3390/bios14040192] [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: 02/15/2024] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Separase is a key cysteine protease in the separation of sister chromatids through the digestion of the cohesin ring that inhibits chromosome segregation as a trigger of the metaphase-anaphase transition in eukaryotes. Its activity is highly regulated by binding with securin and cyclinB-CDK1 complex. These bindings prevent the proteolytic activity of separase until the onset of anaphase. Chromosome missegregation and aneuploidy are frequently observed in malignancies. However, there are some difficulties in biochemical examinations due to the instability of separase in vitro and the fact that few spatiotemporal resolution approaches exist for monitoring live separase activity throughout mitotic processes. Here, we have developed FRET-based molecular sensors, including GFP variants, with separase-cleavable sequences as donors and covalently attached fluorescent dyes as acceptor molecules. These are applicable to conventional live cell imaging and flow cytometric analysis because of efficient live cell uptake. We investigated the performance of equivalent molecular sensors, either localized or not localized inside the nucleus under cell cycle control, using flow cytometry. Synchronized cell cycle progression rendered significant separase activity detections in both molecular sensors. We obtained consistent outcomes with localized molecular sensor introduction and cell cycle control by fluorescent microscopic observations. We thus established live cell separase activity monitoring systems that can be used specifically or statistically, which could lead to the elucidation of separase properties in detail.
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Affiliation(s)
- Md. Shazadur Rahman
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (M.S.R.); (W.I.)
- Department of Agricultural Chemistry, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Yutaka Shindo
- Department of Bioscience and informatics, Faculty of Science and Technology, Keio University, Yokohama 223-0061, Japan; (Y.S.); (K.O.)
| | - Kotaro Oka
- Department of Bioscience and informatics, Faculty of Science and Technology, Keio University, Yokohama 223-0061, Japan; (Y.S.); (K.O.)
- School of Frontier Engineering, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Wataru Ikeda
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (M.S.R.); (W.I.)
| | - Miho Suzuki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (M.S.R.); (W.I.)
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Suzuki M, Shindo Y, Yamanaka R, Oka K. Live imaging of apoptotic signaling flow using tunable combinatorial FRET-based bioprobes for cell population analysis of caspase cascades. Sci Rep 2022; 12:21160. [PMID: 36476686 PMCID: PMC9729311 DOI: 10.1038/s41598-022-25286-z] [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: 05/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding cellular signaling flow is required to comprehend living organisms. Various live cell imaging tools have been developed but challenges remain due to complex cross-talk between pathways and response heterogeneities among cells. We have focused on multiplex live cell imaging for statistical analysis to address the difficulties and developed simple multiple fluorescence imaging system to quantify cell signaling at single-cell resolution using Förster Resonance Energy Transfer (FRET)-based chimeric molecular sensors comprised of fluorescent proteins and dyes. The dye-fluorescent protein conjugate is robust for a wide selection of combinations, facilitating rearrangement for coordinating emission profile of molecular sensors to adjust for visualization conditions, target phenomena, and simultaneous use. As the molecular sensor could exhibit highly sensitive in detection for protease activity, we customized molecular sensor of caspase-9 and combine the established sensor for caspase-3 to validate the system by observation of caspase-9 and -3 dynamics simultaneously, key signaling flow of apoptosis. We found cumulative caspase-9 activity rather than reaction rate inversely regulated caspase-3 execution times for apoptotic cell death. Imaging-derived statistics were thus applied to discern the dominating aspects of apoptotic signaling unavailable by common live cell imaging and proteomics protein analysis. Adopted to various visualization targets, the technique can discriminate between rivalling explanations and should help unravel other protease involved signaling pathways.
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Affiliation(s)
- Miho Suzuki
- grid.263023.60000 0001 0703 3735Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570 Japan
| | - Yutaka Shindo
- grid.26091.3c0000 0004 1936 9959Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Kanagawa, 223-0061 Japan
| | - Ryu Yamanaka
- grid.469470.80000 0004 0617 5071Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Yamaguchi, 756-0884 Japan
| | - Kotaro Oka
- grid.26091.3c0000 0004 1936 9959Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Kanagawa, 223-0061 Japan ,grid.412019.f0000 0000 9476 5696Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan ,grid.5290.e0000 0004 1936 9975Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
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Aktalay A, Ponsot F, Bossi ML, Belov VN, Hell SW. Cleavable Linker Incorporation into a Synthetic Dye-Nanobody-Fluorescent Protein Assembly: FRET, FLIM and STED Microscopy. Chembiochem 2022; 23:e202200395. [PMID: 35838445 PMCID: PMC9804610 DOI: 10.1002/cbic.202200395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Indexed: 01/05/2023]
Abstract
A bright and photostable fluorescent dye with a disulfide (S-S) linker and maleimide group (Rho594-S2-mal), as cleavable and reactive sites, was synthesized and conjugated with anti-GFP nanobodies (NB). The binding of EGFP (FRET donor) with anti-GFP NB labeled with one or two Rho594-S2-mal residues was studied in vitro and in cellulo. The linker was cleaved with dithiothreitol recovering the donor (FP) signal. The bioconjugates (FP-NB-dye) were applied in FRET-FLIM assays, confocal imaging, and superresolution STED microscopy.
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Affiliation(s)
- Ayse Aktalay
- Department of Optical NanoscopyMax Planck Institute for Medical Research (MPI-MR)Jahnstraße 2969120HeidelbergGermany
| | - Flavien Ponsot
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary Sciences (MPI-NAT)Am Fassberg 1137077GöttingenGermany
| | - Mariano L. Bossi
- Department of Optical NanoscopyMax Planck Institute for Medical Research (MPI-MR)Jahnstraße 2969120HeidelbergGermany
| | - Vladimir N. Belov
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary Sciences (MPI-NAT)Am Fassberg 1137077GöttingenGermany
| | - Stefan W. Hell
- Department of Optical NanoscopyMax Planck Institute for Medical Research (MPI-MR)Jahnstraße 2969120HeidelbergGermany,Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary Sciences (MPI-NAT)Am Fassberg 1137077GöttingenGermany
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Mohany NAM, Totti A, Naylor KR, Janovjak H. Microbial methionine transporters and biotechnological applications. Appl Microbiol Biotechnol 2021; 105:3919-3929. [PMID: 33929594 PMCID: PMC8140960 DOI: 10.1007/s00253-021-11307-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 11/07/2022]
Abstract
Methionine (Met) is an essential amino acid with commercial value in animal feed, human nutrition, and as a chemical precursor. Microbial production of Met has seen intensive investigation towards a more sustainable alternative to the chemical synthesis that currently meets the global Met demand. Indeed, efficient Met biosynthesis has been achieved in genetically modified bacteria that harbor engineered enzymes and streamlined metabolic pathways. Very recently, the export of Met as the final step during its fermentative production has been studied and optimized, primarily through identification and expression of microbial Met efflux transporters. In this mini-review, we summarize the current knowledge on four families of Met export and import transporters that have been harnessed for the production of Met and other valuable biomolecules. These families are discussed with respect to their function, gene regulation, and biotechnological applications. We cover methods for identification and characterization of Met transporters as the basis for the further engineering of these proteins and for exploration of other solute carrier families. The available arsenal of Met transporters from different species and protein families provides blueprints not only for fermentative production but also synthetic biology systems, such as molecular sensors and cell-cell communication systems. KEY POINTS: • Sustainable production of methionine (Met) using microbes is actively explored. • Met transporters of four families increase production yield and specificity. • Further applications include other biosynthetic pathways and synthetic biology.
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Affiliation(s)
- Nurul Amira Mohammad Mohany
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Clayton, Australia
- European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Melbourne, Clayton, Australia
| | - Alessandra Totti
- Department of Pharmacy and Biotechnology FaBiT, University of Bologna, Bologna, Italy
| | - Keith R Naylor
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Clayton, Australia
- European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Melbourne, Clayton, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Clayton, Australia.
- European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Melbourne, Clayton, Australia.
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Nichani K, Li J, Suzuki M, Houston JP. Evaluation of Caspase-3 Activity During Apoptosis with Fluorescence Lifetime-Based Cytometry Measurements and Phasor Analyses. Cytometry A 2020; 97:1265-1275. [PMID: 32790129 PMCID: PMC7738394 DOI: 10.1002/cyto.a.24207] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/30/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
Caspase-3 is a well-described protease with many roles that impact the fate of a cell. During apoptosis, caspase-3 acts as an executioner caspase with important proteolytic functions that lead to the final stages of programmed cell death. Owing to this key role, caspase-3 is exploited intracellularly as a target of control of apoptosis for therapeutic outcomes. Yet the activation of caspase-3 during apoptosis is challenged by other roles and functions (e.g., paracrine signaling). This brief report presents a way to track caspase-3 levels using a flow cytometer that measures excited state fluorescence lifetimes and a signal processing approach that leads to a graphical phasor-based interpretation. An established Förster resonance energy transfer (FRET) bioprobe was used for this test; the connected donor and acceptor fluorophore is cleavable by caspase-3 during apoptosis induction. With the cell-by-cell decay kinetic data and phasor analyses we generate a caspase activation trajectory, which is used to interpret activation throughout apoptosis. When lifetime-based cytometry is combined with a FRET bioprobe and phasor analyses, enzyme activation can be simplified and quantified with phase and modulation data. We envision extrapolating this approach to high content screening, and reinforce the power of phasor approaches with cytometric data. Analyses such as these can be used to cluster cells by their phase and modulation "lifetime fingerprint" when the intracellular fluorescent probe is utilized as a sensor of enzyme activity. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Kapil Nichani
- Department of Chemical & Materials EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Jianzhi Li
- Department of Chemical & Materials EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Miho Suzuki
- Department of Functional Materials and ScienceGraduate School of Science and Engineering, Saitama UniversitySaitama338‐8570Japan
| | - Jessica P. Houston
- Department of Chemical & Materials EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
- Department of Functional Materials and ScienceGraduate School of Science and Engineering, Saitama UniversitySaitama338‐8570Japan
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Detection and Quantitative Analysis of Dynamic GPCRs Interactions Using Flow Cytometry-Based FRET. RECEPTOR-RECEPTOR INTERACTIONS IN THE CENTRAL NERVOUS SYSTEM 2018. [DOI: 10.1007/978-1-4939-8576-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Method for Developing Optical Sensors Using a Synthetic Dye-Fluorescent Protein FRET Pair and Computational Modeling and Assessment. Methods Mol Biol 2017; 1596:89-99. [PMID: 28293882 DOI: 10.1007/978-1-4939-6940-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Biosensors that exploit Förster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors.
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Suzuki M, Sakata I, Sakai T, Tomioka H, Nishigaki K, Tramier M, Coppey-Moisan M. A high-throughput direct fluorescence resonance energy transfer-based assay for analyzing apoptotic proteases using flow cytometry and fluorescence lifetime measurements. Anal Biochem 2015; 491:10-7. [DOI: 10.1016/j.ab.2015.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 01/27/2023]
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Shi Y, Yi C, Zhang Z, Zhang H, Li M, Yang M, Jiang Q. Peptide-bridged assembly of hybrid nanomaterial and its application for caspase-3 detection. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6494-6501. [PMID: 23806127 DOI: 10.1021/am401935y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent developments in the rational design and the controlled assembly of nanoscale building blocks have resulted in functional devices such as nano-optoelectronics, novel contrast probes for molecular imaging, and nanosensors. In the present study, we designed and synthesized a hybrid nanomaterial consisting of [Ru(bpy)3](2+)-encapsulated silica nanoparticles (SiNPs) and gold nanoparticles (AuNPs) through peptide-bridged assembly in a controllable way. A peptide that contains recognition sequence DEVD specific for active caspase-3 cleavage was employed to bring SiNPs and AuNPs into close proximity through specific molecular recognition. A FRET system with SiNPs as energy donors and AuNPs as energy acceptors has been thus developed and applied for caspase-3 detection. A change in distance between the two building blocks resulted in a change in FRET efficiency, causing a ratiometric change in emission. Caspase-3 triggers the cleavage of the peptide links between the two nanoparticles and releases AuNPs from the nanohybrids, inducing the activation of SiNPs to the "ON" state. The fluorescence turn-on response is specific to caspase-3 and allows the detection of caspase-3 as low as 0.05 U mL(-1) (∼6 pM).
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Affiliation(s)
- Yupeng Shi
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Engineering, Sun Yat-Sen University, Guangzhou, China
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