1
|
Reja SI, Minoshima M, Hori Y, Kikuchi K. Development of an effective protein-labeling system based on smart fluorogenic probes. J Biol Inorg Chem 2019; 24:443-455. [PMID: 31152238 DOI: 10.1007/s00775-019-01669-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022]
Abstract
Proteins are an important component of living systems and play a crucial role in various physiological functions. Fluorescence imaging of proteins is a powerful tool for monitoring protein dynamics. Fluorescent protein (FP)-based labeling methods are frequently used to monitor the movement and interaction of cellular proteins. However, alternative methods have also been developed that allow the use of synthetic fluorescent probes to target a protein of interest (POI). Synthetic fluorescent probes have various advantages over FP-based labeling methods. They are smaller in size than the fluorescent proteins, offer a wide variety of colors and have improved photochemical properties. There are various chemical recognition-based labeling techniques that can be used for labeling a POI with a synthetic probe. In this review, we focus on the development of protein-labeling systems, particularly the SNAP-tag, BL-tag, and PYP-tag systems, and understanding the fluorescence behavior of the fluorescently labeled target protein in these systems. We also discuss the smart fluorogenic probes for these protein-labeling systems and their applications. The fluorogenic protein labeling will be a useful tool to investigate complex biological phenomena in future work on cell biology.
Collapse
Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
2
|
Mosaiab T, In I, Park SY. Temperature and pH-Tunable Fluorescence Nanoplatform with Graphene Oxide and BODIPY-Conjugated Polymer for Cell Imaging and Therapy. Macromol Rapid Commun 2013; 34:1408-15. [DOI: 10.1002/marc.201300413] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/05/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Tamim Mosaiab
- Department of Green Bio Engineering; Korea National University of Transportation; Chungju-Si 380-702 Republic of Korea
| | - Insik In
- Department of Polymer Science and Engineering; Korea National University of Transportation; Chungju-Si 380-702 Republic of Korea
| | - Sung Y. Park
- Department of Chemical and Biological Engineering and Department of Green Bio Engineering; Korea National University of Transportation; Chungju-Si 380-702 Republic of Korea
| |
Collapse
|
3
|
A bilirubin-inducible fluorescent protein from eel muscle. Cell 2013; 153:1602-11. [PMID: 23768684 DOI: 10.1016/j.cell.2013.05.038] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 05/14/2013] [Accepted: 05/17/2013] [Indexed: 01/30/2023]
Abstract
The fluorescent protein toolbox has revolutionized experimental biology. Despite this advance, no fluorescent proteins have been identified from vertebrates, nor has chromogenic ligand-inducible activation or clinical utility been demonstrated. Here, we report the cloning and characterization of UnaG, a fluorescent protein from Japanese eel. UnaG belongs to the fatty-acid-binding protein (FABP) family, and expression in eel is restricted to small-diameter muscle fibers. On heterologous expression in cell lines or mouse brain, UnaG produces oxygen-independent green fluorescence. Remarkably, UnaG fluorescence is triggered by an endogenous ligand, bilirubin, a membrane-permeable heme metabolite and clinical health biomarker. The holoUnaG structure at 1.2 Å revealed a biplanar coordination of bilirubin by reversible π-conjugation, and we used this high-affinity and high-specificity interaction to establish a fluorescence-based human bilirubin assay with promising clinical utility. UnaG will be the prototype for a versatile class of ligand-activated fluorescent proteins, with applications in research, medicine, and bioengineering.
Collapse
|
4
|
Romieu A, Massif C, Rihn S, Ulrich G, Ziessel R, Renard PY. The first comparative study of the ability of different hydrophilic groups to water-solubilise fluorescent BODIPY dyes. NEW J CHEM 2013. [DOI: 10.1039/c3nj41093e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
5
|
Kocaoglu O, Calvo RA, Sham LT, Cozy LM, Lanning BR, Francis S, Winkler ME, Kearns DB, Carlson EE. Selective penicillin-binding protein imaging probes reveal substructure in bacterial cell division. ACS Chem Biol 2012; 7:1746-53. [PMID: 22909777 PMCID: PMC3663142 DOI: 10.1021/cb300329r] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The peptidoglycan cell wall is a common target for antibiotic therapy, but its structure and assembly are only partially understood. Peptidoglycan synthesis requires a suite of penicillin-binding proteins (PBPs), the individual roles of which are difficult to determine because each enzyme is often dispensable for growth perhaps due to functional redundancy. To address this challenge, we sought to generate tools that would enable selective examination of a subset of PBPs. We designed and synthesized fluorescent and biotin derivatives of the β-lactam-containing antibiotic cephalosporin C. These probes facilitated specific in vivo labeling of active PBPs in both Bacillus subtilis PY79 and an unencapsulated derivative of D39 Streptococcus pneumoniae. Microscopy and gel-based analysis indicated that the cephalosporin C-based probes are more selective than BOCILLIN-FL, a commercially available penicillin V analogue, which labels all PBPs. Dual labeling of live cells performed by saturation of cephalosporin C-susceptible PBPs followed by tagging of the remaining PBP population with BOCILLIN-FL demonstrated that the two sets of PBPs are not co-localized. This suggests that even PBPs that are located at a particular site (e.g., septum) are not all intermixed, but rather that PBP subpopulations are discretely localized. Accordingly, the Ceph C probes represent new tools to explore a subset of PBPs and have the potential to facilitate a deeper understand of the roles of this critical class of proteins.
Collapse
Affiliation(s)
- Ozden Kocaoglu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Rebecca A. Calvo
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Lok-To Sham
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Loralyn M. Cozy
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Bryan R. Lanning
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Samson Francis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Erin E. Carlson
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
6
|
Mizukami S. Development of molecular imaging tools to investigate protein functions by chemical probe design. Chem Pharm Bull (Tokyo) 2012; 59:1435-46. [PMID: 22130363 DOI: 10.1248/cpb.59.1435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular imaging technologies, which enable the visualization of the behaviors or functions of biomolecules in living systems, have received considerable attention from life scientists. Novel imaging technologies that overcome the limitations of current imaging techniques are desired. In this review, two independent technologies that were recently developed by the authors are described. The first technology is for smart (19)F magnetic resonance imaging (MRI) probes that were developed for in vivo applications. These probes were developed by exploiting paramagnetic relaxation enhancement in order to detect hydrolase activity. With respect to cellular applications, gene expression in cells was visualized using one of the (19)F MRI probes. It was confirmed that this probe design principle is effective for various hydrolases, and broad applications are expected. The second technology is for practical protein labeling. This labeling method is based on a mutant β-lactamase and its specific labeling probes. Since the probe is fluorescence resonance energy transfer (FRET)-based, this labeling method achieves both specific and fluorogenic labeling of target proteins. In addition, derivatization of the probe enabled the labeling of intracellular proteins and the modification of various functional molecules.
Collapse
Affiliation(s)
- Shin Mizukami
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.
| |
Collapse
|
7
|
Sadhu KK, Mizukami S, Lanam CR, Kikuchi K. Fluorogenic Protein Labeling through Photoinduced Electron Transfer-Based BL-Tag Technology. Chem Asian J 2011; 7:272-6. [DOI: 10.1002/asia.201100647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Indexed: 11/09/2022]
|
8
|
Jewett JC, Bertozzi CR. Synthesis of a fluorogenic cyclooctyne activated by Cu-free click chemistry. Org Lett 2011; 13:5937-9. [PMID: 22029411 DOI: 10.1021/ol2025026] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cyclooctyne-based probes that become fluorescent upon reaction with azides are important targets for real-time imaging of azide-labeled biomolecules. The concise synthesis of a coumarin-conjugated cyclooctyne, coumBARAC, that undergoes a 10-fold enhancement in fluorescence quantum yield upon triazole formation with organic azides is reported. The design principles embodied in coumBARAC establish a platform for generating fluorogenic cyclooctynes suited for biological imaging.
Collapse
Affiliation(s)
- John C Jewett
- Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | | |
Collapse
|
9
|
Kowada T, Kikuta J, Kubo A, Ishii M, Maeda H, Mizukami S, Kikuchi K. In Vivo Fluorescence Imaging of Bone-Resorbing Osteoclasts. J Am Chem Soc 2011; 133:17772-6. [DOI: 10.1021/ja2064582] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toshiyuki Kowada
- Laboratory of Chemical Imaging Techniques, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
| | - Junichi Kikuta
- Laboratory of Cellular Dynamics, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
- Japan Science and Technology Agency (JST), CREST, Tokyo, Japan
| | - Atsuko Kubo
- Laboratory of Cellular Dynamics, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
- Japan Science and Technology Agency (JST), CREST, Tokyo, Japan
| | - Masaru Ishii
- Laboratory of Cellular Dynamics, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
- Japan Science and Technology Agency (JST), CREST, Tokyo, Japan
| | - Hiroki Maeda
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Shin Mizukami
- Laboratory of Chemical Imaging Techniques, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Kazuya Kikuchi
- Laboratory of Chemical Imaging Techniques, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka, Japan
| |
Collapse
|