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Li SA, Meng XY, Zhang YJ, Chen CL, Jiao YX, Zhu YQ, Liu PP, Sun W. Progress in pH-Sensitive sensors: essential tools for organelle pH detection, spotlighting mitochondrion and diverse applications. Front Pharmacol 2024; 14:1339518. [PMID: 38269286 PMCID: PMC10806205 DOI: 10.3389/fphar.2023.1339518] [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: 11/16/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
pH-sensitive fluorescent proteins have revolutionized the field of cellular imaging and physiology, offering insight into the dynamic pH changes that underlie fundamental cellular processes. This comprehensive review explores the diverse applications and recent advances in the use of pH-sensitive fluorescent proteins. These remarkable tools enable researchers to visualize and monitor pH variations within subcellular compartments, especially mitochondria, shedding light on organelle-specific pH regulation. They play pivotal roles in visualizing exocytosis and endocytosis events in synaptic transmission, monitoring cell death and apoptosis, and understanding drug effects and disease progression. Recent advancements have led to improved photostability, pH specificity, and subcellular targeting, enhancing their utility. Techniques for multiplexed imaging, three-dimensional visualization, and super-resolution microscopy are expanding the horizon of pH-sensitive protein applications. The future holds promise for their integration into optogenetics and drug discovery. With their ever-evolving capabilities, pH-sensitive fluorescent proteins remain indispensable tools for unravelling cellular dynamics and driving breakthroughs in biological research. This review serves as a comprehensive resource for researchers seeking to harness the potential of pH-sensitive fluorescent proteins.
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Affiliation(s)
- Shu-Ang Li
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Yan Meng
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Jie Zhang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Li Chen
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yu-Xue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Qing Zhu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pei-Pei Liu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Sun
- Department of Burn and Repair Reconstruction, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Jimbo M, Otake M, Amano H, Yasumoto K, Watabe S, Okada D, Kumagai H. Characterization of recombinant photoconverting green fluorescent Akanes. J Biochem 2023; 175:25-34. [PMID: 37812399 DOI: 10.1093/jb/mvad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
Akanes are fluorescent proteins that have several fluorescence maxima. In this report, Akane1 and Akane3 from Scleronephthya gracillima were selected, successfully overexpressed in Escherichia coli and purified by affinity chromatography. Fluorescence spectra of the recombinant Akanes matured in darkness, or ambient light were found to have several fluorescence peaks. SDS-PAGE analysis revealed that Akanes matured in ambient light have two fragments. MS/MS analysis of Akanes digested with trypsin showed that the cleavage site is the same as observed for the photoconvertible fluorescent protein Kaede. The differences between the calculated masses from the amino acid sequence of Akane1 and the measured masses of Akane1 fragments obtained under ambient light coincided with those of Kaede. In contrast, a mass difference between the measured N-terminal Akane3 fragment and the calculated mass indicated that Akane3 is modified in the N-terminal region. These results indicate that numerous peaks in the fluorescent spectra of Akanes partly arise from isoproteins of Akanes and photoconversion. Photoconversion of Akane1 caused a fluorescence change from green to red, which was also observed for Akane3; however, the fluorescent intensity decreased dramatically when compared with that of Akane3.
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Affiliation(s)
- Mitsuru Jimbo
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Mayumi Otake
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Haruna Amano
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Daisuke Okada
- School of Medicine, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Hiroshi Kumagai
- School of Allied Health Sciences, Kitasato University. 1-15-1, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
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Metal-Induced Fluorescence Quenching of Photoconvertible Fluorescent Protein DendFP. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092922. [PMID: 35566273 PMCID: PMC9104182 DOI: 10.3390/molecules27092922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 12/29/2022]
Abstract
Sensitive and accurate detection of specific metal ions is important for sensor development and can advance analytical science and support environmental and human medical examinations. Fluorescent proteins (FPs) can be quenched by specific metal ions and spectroscopically show a unique fluorescence-quenching sensitivity, suggesting their potential application as FP-based metal biosensors. Since the characteristics of the fluorescence quenching are difficult to predict, spectroscopic analysis of new FPs is important for the development of FP-based biosensors. Here we reported the spectroscopic and structural analysis of metal-induced fluorescence quenching of the photoconvertible fluorescent protein DendFP. The spectroscopic analysis showed that Fe2+, Fe3+, and Cu2+ significantly reduced the fluorescence emission of DendFP. The metal titration experiments showed that the dissociation constants (Kd) of Fe2+, Fe3+, and Cu2+ for DendFP were 24.59, 41.66, and 137.18 μM, respectively. The tetrameric interface of DendFP, which the metal ions cannot bind to, was analyzed. Structural comparison of the metal-binding sites of DendFP with those of iq-mEmerald and Dronpa suggested that quenchable DendFP has a unique metal-binding site on the β-barrel that does not utilize the histidine pair for metal binding.
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Frolova AY, Pakhomov AA, Martynov VI. Physicochemical Properties of Photoconvertible Fluorescent Protein from Montastraea cavernosa. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Fluorescent Tags in Biology: Three-Dimensional Structure. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pakhomov AA, Frolova AY, Tabakmakher VM, Chugunov AO, Efremov RG, Martynov VI. Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 206:111853. [PMID: 32272363 DOI: 10.1016/j.jphotobiol.2020.111853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/27/2020] [Accepted: 03/13/2020] [Indexed: 11/16/2022]
Abstract
The precise positioning of catalytic amino acids against the substrate in an enzyme active site is a crucial factor in biocatalysis. Biosynthesis of the chromophores of fluorescent proteins (FPs) is an autocatalytic process that must conform to these requirements. Here, we show that, in addition to the internal amino acid residues in the proximity of the chromophore, chromophore biosynthesis is influenced by the remote amino acids exposed on the outer surface of the β-barrel structure of the FP. It has been shown earlier that chromophore biosynthesis of the red FP from Zoanthus sp. (zoan2RFP) proceeds via an immature green state. At the same time, the green state is the final stage of chromophore biosynthesis of green FP (zoanGFP), which is highly homologous to zoan2RFP. It was also shown that a single N66D substitution in the chromophore-forming sequence of zoanGFP might trigger the synthesis of the red chromophore. However, in this case, the synthesis of the red chromophore is incomplete and occurs only at elevated temperatures. Here, we tried to uncover additional structural determinants that govern the biosynthesis of the red chromophore. A comparison of zoanGFP and zoan2RFP revealed intrabarrel amino acid differences at five positions. Exhaustive substitutions of these five positions in zoanGFP-N66D gave rise to zoanGFPmut with the same intrabarrel amino acid composition as zoan2RFP. zoanGFPmut showed only partial green-to-red chromophore transformation at elevated temperatures. To elucidate the extra factors that can affect red chromophore biosynthesis, we performed comparative molecular dynamics simulations of zoan2RFP and zoanGFPmut. The simulations revealed several external amino acids that might influence the arrangement and flexibility of the chromophore-surrounding amino acid residues in these proteins. Mutagenesis experiments confirmed the crucial role of these residues in red chromophore biosynthesis. The obtained zoanGFPmut2 exhibited complete green-to-red transformation, suggesting that the mutated amino acids exposed on the surface of the β-barrel contribute to red chromophore biosynthesis.
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Affiliation(s)
- Alexey A Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; A.N. Nesmeyanov Institute of Organoelement Compounds, Moscow 119334, Russia.
| | - Anastasiya Yu Frolova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; A.N. Nesmeyanov Institute of Organoelement Compounds, Moscow 119334, Russia
| | - Valentin M Tabakmakher
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; School of Biomedicine, Far Eastern Federal University, Vladivostok 690950, Russia
| | - Anton O Chugunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research University Higher School of Economics, Moscow 101000, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Moscow Oblast, Russia
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research University Higher School of Economics, Moscow 101000, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Moscow Oblast, Russia
| | - Vladimir I Martynov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Structure of Chromophores in GFP-Like Proteins: X-Ray Data. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201903004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pakhomov AA, Martynov VI, Orsa AN, Bondarenko AA, Chertkova RV, Lukyanov KA, Petrenko AG, Deyev IE. Fluorescent protein Dendra2 as a ratiometric genetically encoded pH-sensor. Biochem Biophys Res Commun 2017; 493:1518-1521. [PMID: 28986251 DOI: 10.1016/j.bbrc.2017.09.170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/30/2017] [Indexed: 10/18/2022]
Abstract
Fluorescent protein Dendra2 is a monomeric GFP-like protein that belongs to the group of Kaede-like photoconvertible fluorescent proteins with irreversible photoconversion from a green- to red-emitting state when exposed to violet-blue light. In an acidic environment, photoconverted Dendra2 turns green due to protonation of the phenolic group of the chromophore with pKa of about 7.5. Thus, photoconverted form of Dendra2 can be potentially used as a ratiometric pH-sensor in the physiological pH range. However, incomplete photoconversion makes ratiometric measurements irreproducible when using standard filter sets. Here, we describe the method to detect fluorescence of only photoconverted Dendra2 form, but not nonconverted green Dendra2. We show that the 350 nm excitation light induces solely the fluorescence of photoconverted protein. By measuring the red to green fluorescence ratio, we determined intracellular pH in live CHO and HEK 293 cells. Thus, Dendra2 can be used as a novel ratiometric genetically encoded pH sensor with emission maxima in the green-red spectral region, which is suitable for application in live cells.
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Affiliation(s)
- Alexey A Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Vladimir I Martynov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander N Orsa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alena A Bondarenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Rita V Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander G Petrenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Igor E Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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Pakhomov AA, Chertkova RV, Deyev IE, Petrenko AG, Martynov VI. Generation of photoactivatable fluorescent protein from photoconvertible ancestor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s106816201703013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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