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Ikeda T, Nakasugi Y, Nakagawa M, Matsuura SI, Ikeda T, Ishida T, Funabashi H, Hirota R, Kuroda A. Discovery of long-chain polyamines embedded in the biosilica on the Bacillus cereus spore coat. J Biosci Bioeng 2024; 137:254-259. [PMID: 38342665 DOI: 10.1016/j.jbiosc.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/13/2024]
Abstract
Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification has only recently begun to be studied. We previously reported that biosilicification occurs in the gram-positive, spore-forming bacterium Bacillus cereus, and that silica is intracellularly deposited on the spore coat as a protective coating against acids, although the underlying mechanism is not yet fully understood. In eukaryotic biosilicifying organisms, such as diatoms and siliceous sponges, several relevant biomolecules are embedded in biogenic silica (biosilica). These biomolecules include peptides, proteins, and long-chain polyamines. In this study, we isolated organic compounds embedded in B. cereus biosilica to investigate the biomolecules involved in the prokaryotic biosilicification process and identified long-chain polyamines with a chemical structure of H2N-(CH2)4-[NH-(CH2)3]n-NH2 (n: up to 55). Our results demonstrate the common presence of long-chain polyamines in different evolutionary lineages of biosilicifying organisms, i.e., diatoms, siliceous sponges, and B. cereus, suggesting a common mechanism underlying eukaryotic and prokaryotic biosilicification.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Yukihide Nakasugi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Miki Nakagawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Shun-Ichi Matsuura
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takuji Ikeda
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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Masaki K, Ahmed ABF, Ishida T, Mikami Y, Funabashi H, Hirota R, Ikeda T, Kuroda A. Chromatographic purification of small extracellular vesicles using an affinity column for phospholipid membranes. Biotechnol Lett 2023; 45:1457-1466. [PMID: 37787831 PMCID: PMC10635940 DOI: 10.1007/s10529-023-03430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/01/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
OBJECTIVES This study aimed to investigate whether chromatography using an ExoPUA column, an affinity column for phospholipid membranes, could potentially serve as an efficient, rapid, scalable, and reproducible method for purifying small extracellular vesicles (sEVs). RESULTS We used the ExoPUA column connected to a fast-performance liquid chromatography system. One-step chromatographic purification of sEVs from culture supernatant using the ExoPUA protocol resulted in an 82 ± 16-fold increase in purity with a yield of 38 ± 5% of sEVs. The purified sEVs contained CD9, CD63, TSG101, and miRNA (miR-21), but not the endoplasmic reticulum protein Calnexin. Transmission electron microscopy indicated that the purified sEVs were intact. The purification performance of the ExoPUA protocol showed superior results in terms of yield compared to that of the differential ultracentrifugation method, the most commonly used method for purifying sEVs in laboratories, and purity compared to that of the DEAE chromatography protocol. CONCLUSION The sEVs were effectively purified in the bind-elute mode and the ExoPUA column can be refreshed and sterilized with sodium hydroxide (NaOH), having high potential for multiple sEV purification in a scalable and industrial manner.
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Affiliation(s)
- Kanako Masaki
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Abo Bakr F Ahmed
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Yuuki Mikami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan.
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Abdel-Hady GN, Tajima T, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. A novel salt- and organic solvent-tolerant phosphite dehydrogenase from Cyanothece sp. ATCC 51142. Front Bioeng Biotechnol 2023; 11:1255582. [PMID: 37662428 PMCID: PMC10473253 DOI: 10.3389/fbioe.2023.1255582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Phosphite dehydrogenase (PtxD) is a promising enzyme for NAD(P)H regeneration. To expand the usability of PtxD, we cloned, expressed, and analyzed PtxD from the marine cyanobacterium Cyanothece sp. ATCC 51142 (Ct-PtxD). Ct-PtxD exhibited maximum activity at pH 9.0°C and 50°C and high stability over a wide pH range of 6.0-10.0. Compared to previously reported PtxDs, Ct-PtxD showed increased resistance to salt ions such as Na+, K+, and NH4 +. It also exhibited high tolerance to organic solvents such as ethanol, dimethylformamide, and methanol when bound to its preferred cofactor, NAD+. Remarkably, these organic solvents enhanced the Ct-PtxD activity while inhibiting the PtxD activity of Ralstonia sp. 4506 (Rs-PtxD) at concentrations ranging from 10% to 30%. Molecular electrostatic potential analysis showed that the NAD+-binding site of Ct-PtxD was rich in positively charged residues, which may attract the negatively charged pyrophosphate group of NAD+ under high-salt conditions. Amino acid composition analysis revealed that Ct-PtxD contained fewer hydrophobic amino acids than other PtxD enzymes, which reduced the hydrophobicity and increased the hydration of protein surface under low water activity. We also demonstrated that the NADH regeneration system using Ct-PtxD is useful for the coupled chiral conversion of trimethylpyruvic acid into L-tert-leucine using leucine dehydrogenase under high ammonium conditions, which is less supported by the Rs-PtxD enzyme. These results imply that Ct-PtxD might be a potential candidate for NAD(P)H regeneration in industrial applications under the reaction conditions containing salt and organic solvent.
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Affiliation(s)
- Gamal Nasser Abdel-Hady
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Department of Genetics, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Takahisa Tajima
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
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Hirota R, Katsuura ZI, Momokawa N, Murakami H, Watanabe S, Ishida T, Ikeda T, Funabashi H, Kuroda A. Gatekeeper Residue Replacement in a Phosphite Transporter Enhances Mutational Robustness of the Biocontainment Strategy. ACS Synth Biol 2022; 11:3397-3404. [PMID: 36202772 DOI: 10.1021/acssynbio.2c00296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Biocontainment is a key methodology to reduce environmental risk through the deliberate release of genetically modified microorganisms. Previously, we developed a phosphite (HPO32-)-dependent biocontainment strategy, by expressing a phosphite-specific transporter HtxBCDE and phosphite dehydrogenase in bacteria devoid of their indigenous phosphate (HPO42-) transporters. This strategy did not allow Escherichia coli to generate escape mutants (EMs) in growth media containing phosphate as a phosphorus source using an assay with a detection limit of 1.9 × 10-13. In this study, we found that the coexistence of a high dose of phosphate (>0.5 mM) with phosphite in the growth medium allows the phosphite-dependent E. coli strain to generate EMs at a frequency of approximately 5.4 × 10-10. In all EMs, the mutation was a single amino acid substitution of phenylalanine to cysteine or serine at position 210 of HtxC, the transmembrane domain protein of the phosphorus compound transporter HtxBCDE. Replacement of the HtxC F210 residue with the other 17 amino acids revealed that HtxC F210 is crucial in determining substrate specificity of HtxBCDE. Based on the finding of the role of HtxC F210 as a "gatekeeper" residue for this transporter, we demonstrate that the replacement of HtxC F210 with amino acids resulting from codons that require two simultaneous point mutations to generate phosphate permissive HtxC mutants can reduce the rate of EM generation to an undetectable level. These findings also provide novel insights into the functional classification of HtxBCDE as a noncanonical ATP-binding cassette transporter in which the transmembrane domain protein participates in substrate recognition.
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Affiliation(s)
- Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Zen-Ichiro Katsuura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Naoki Momokawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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5
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Motomura K, Sano K, Watanabe S, Kanbara A, Abdel-Hady GN, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Correction to "Synthetic Phosphorus Metabolic Pathway for Biosafety and Contamination Management of Cyanobacterial Cultivation". ACS Synth Biol 2021; 10:1797. [PMID: 34152128 DOI: 10.1021/acssynbio.1c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Abdel-Hady GN, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Engineering Cofactor Specificity of a Thermostable Phosphite Dehydrogenase for a Highly Efficient and Robust NADPH Regeneration System. Front Bioeng Biotechnol 2021; 9:647176. [PMID: 33869158 PMCID: PMC8047080 DOI: 10.3389/fbioe.2021.647176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADP)-dependent dehydrogenases catalyze a range of chemical reactions useful for practical applications. However, their dependence on the costly cofactor, NAD(P)H remains a challenge which must be addressed. Here, we engineered a thermotolerant phosphite dehydrogenase from Ralstonia sp. 4506 (RsPtxD) by relaxing the cofactor specificity for a highly efficient and robust NADPH regeneration system. The five amino acid residues, Cys174-Pro178, located at the C-terminus of β7-strand region in the Rossmann-fold domain of RsPtxD, were changed by site-directed mutagenesis, resulting in four mutants with a significantly increased preference for NADP. The catalytic efficiency of mutant RsPtxDHARRA for NADP (K cat/K M)NADP was 44.1 μM-1 min-1, which was the highest among the previously reported phosphite dehydrogenases. Moreover, the RsPtxDHARRA mutant exhibited high thermostability at 45°C for up to 6 h and high tolerance to organic solvents, when bound with NADP. We also demonstrated the applicability of RsPtxDHARRA as an NADPH regeneration system in the coupled reaction of chiral conversion of 3-dehydroshikimate to shikimic acid by the thermophilic shikimate dehydrogenase of Thermus thermophilus HB8 at 45°C, which could not be supported by the parent RsPtxD enzyme. Therefore, the RsPtxDHARRA mutant might be a promising alternative NADPH regeneration system for practical applications.
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Affiliation(s)
- Gamal Nasser Abdel-Hady
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Department of Genetics, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.,Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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Ishida T, Hashimoto T, Masaki K, Funabashi H, Hirota R, Ikeda T, Tajima H, Kuroda A. Application of peptides with an affinity for phospholipid membranes during the automated purification of extracellular vesicles. Sci Rep 2020; 10:18718. [PMID: 33127950 PMCID: PMC7603496 DOI: 10.1038/s41598-020-75561-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 10/15/2020] [Indexed: 01/02/2023] Open
Abstract
Extracellular vesicles (EVs), such as exosomes, have garnered increasing interest because of their potential clinical applications that range from diagnostics to therapeutics. The development of an automated and reproducible EV purification platform would therefore aid the introduction of EV biomarkers and therapies into the clinic. Here, we demonstrate that K8- as well as K-16 peptides (containing 8 and 16 lysine residues with dissociation constants of 102 nM and 11.6 nM for phosphatidylserine, respectively) immobilized on magnetic beads can capture small EVs (< 0.2 µm) from culture supernatants of MCF7 human breast cancer cells. Importantly, the bound EVs could be dissociated from the beads under mild conditions (e.g. 0.5 M NaCl), and the isolated EVs had the typical shapes of EVs under SEM and TEM with a mean particle size of 99 nm. Using the peptide-immobilized beads, we adapted a pre-existing bench top instrument for magnetic separation to perform automated EV purification with higher purity and yield than that obtained using the standard ultracentrifugation method.
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Affiliation(s)
- Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Takuma Hashimoto
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Kanako Masaki
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Hideji Tajima
- Precision System Science Co., Ltd., 88 Kamihongo, Matsudo, Chiba, 271-0064, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan.
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Hino S, Sugikawa K, Kawasaki R, Funabashi H, Kuroda A, Ikeda A. Aggregation‐Induced Emission and Retention of Crystal Chiral Information of Tetraphenylethylene Incorporated by Polysaccharides in Water. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Shodai Hino
- Department of Applied ChemistryGraduate School of Engineering, Hiroshima University 1-4-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8527 Japan
| | - Kouta Sugikawa
- Department of Applied ChemistryGraduate School of Engineering, Hiroshima University 1-4-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8527 Japan
| | - Riku Kawasaki
- Department of Applied ChemistryGraduate School of Engineering, Hiroshima University 1-4-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8527 Japan
| | - Hisakage Funabashi
- Department of Molecular BiotechnologyGraduate School of Advanced Sciences of Matter Hiroshima University 1-3-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8530 Japan
| | - Akio Kuroda
- Department of Molecular BiotechnologyGraduate School of Advanced Sciences of Matter Hiroshima University 1-3-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8530 Japan
| | - Atsushi Ikeda
- Department of Applied ChemistryGraduate School of Engineering, Hiroshima University 1-4-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8527 Japan
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Ikeda T, Ichikawa K, Shigeto H, Ishida T, Hirota R, Funabashi H, Kuroda A. Arginine-mediated dissociation of single cells and cell sheets from a polystyrene culture dish. Biosci Biotechnol Biochem 2019; 83:2272-2275. [PMID: 31482750 DOI: 10.1080/09168451.2019.1659716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Here, we report a novel non-enzymatic cell dissociation method, based on our finding that adherent cells dissociate rapidly from the polystyrene culture dish when incubated in an l- or d-arginine-containing solution. We also demonstrate the successful detachment of confluent NIH/3T3 cell monolayers from the culture dish as a cell sheet by the addition of an arginine solution.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kohei Ichikawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hajime Shigeto
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan.,Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
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Ishida T, Fujihara N, Nishimura T, Funabashi H, Hirota R, Ikeda T, Kuroda A. Live-cell imaging of macrophage phagocytosis of asbestos fibers under fluorescence microscopy. Genes Environ 2019; 41:14. [PMID: 31178942 PMCID: PMC6549298 DOI: 10.1186/s41021-019-0129-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background Frustrated phagocytosis occurs when an asbestos fiber > 10 μm in length is engulfed imperfectly by a macrophage, and it is believed to be associated with chromosomal instability. Few studies have focused on dynamic cellular imaging to assess the toxicity of hazardous inorganic materials such as asbestos. One reason for this is the relative lack of fluorescent probes available to facilitate experimental visualization of inorganic materials. We recently developed asbestos-specific fluorescent probes based on asbestos-binding proteins, and achieved efficient fluorescent labeling of asbestos. Results Live-cell imaging with fluorescent asbestos probes was successfully utilized to dynamically analyze asbestos phagocytosis. The fluorescently labeled asbestos fibers were phagocytosed by RAW 264.7 macrophages. Internalized fibers of < 5 μm in length were visualized clearly via overlaid phase contrast and fluorescence microscopy images, but they were not clearly depicted using phase contrast images alone. Approximately 60% of the cells had phagocytosed asbestos fibers after 2 h, but over 96% of cells remained alive even 24 h after the addition of asbestos fibers. Immediate cell death was only observed when an asbestos fiber was physically pulled from a cell by an external force. Notably, at 24 h after the addition of asbestos fibers an approximately 4-fold increase in the number of binucleated cells was observed. Monitoring of individual cell divisions of cells that had phagocytosed asbestos suggested that binucleated cells were formed via the inhibition of cell separation, by asbestos fibers of > 10 μm in length that were localized in the proximity of the intercellular bridge. Conclusions Fluorescently labeled asbestos facilitated visualization of the dynamic biological processes that occur during and after the internalization of asbestos fibers, and indicated that (i) frustrated phagocytosis itself does not lead to immediate cell death unless the asbestos fiber is physically pulled from the cell by an external force, and (ii) macrophages that have phagocytosed asbestos can divide but sometimes the resulting daughter cells fuse, leading to the formation of a binucleated cell. This fusion only seemed to occur when a comparatively long asbestos fiber (> 10 μm) was shared by two daughter cells.
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Affiliation(s)
- Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
| | - Nobutoshi Fujihara
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
| | - Tomoki Nishimura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi Hiroshima, Hiroshima, 739-8530 Japan
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11
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Shigeto H, Ono T, Ikeda T, Hirota R, Ishida T, Kuroda A, Funabashi H. Insulin sensor cells for the analysis of insulin secretion responses in single living pancreatic β cells. Analyst 2019; 144:3765-3772. [PMID: 31089611 DOI: 10.1039/c9an00405j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigation of the functions of insulin-secreting cells in response to glucose in single-living cells is essential for improving our knowledge on the pathogenesis of diabetes. Therefore, it is desired to develop a new convenient method that enables the direct detection of insulin secreted from single-living cells. Here, insulin-sensor-cells expressing a protein-based insulin-detecting probe immobilized on the extracellular membrane were developed to evaluate the insulin-secretion response in single-living pancreatic β cells. The protein-based insulin-detecting probe (NαLY) was composed of a bioluminescent protein (nano-luc), the αCT segment of the insulin receptor, L1 and CR domains of the insulin receptor, and a fluorescent protein (YPet). NαLY exhibited a bioluminescence resonance energy transfer (BRET) signal in response to insulin; thus, cells of Hepa1-6 line were genetically engineered to express NαLY on the extracellular membrane. The cells were found to act as insulin-sensor-cells, exhibiting a BRET signal in response to insulin. When the insulin-sensor-cells and pancreatic β cells (MIN6 cell line) were cocultured and stimulated with glucose, insulin-sensor-cells nearby pancreatic β cells showed the spike-shaped BRET signal response, whereas the insulin-sensor-cells close to one pancreatic β cell did not exhibit such signal response. However, all the insulin-sensor-cells showed a gradual increase in BRET signals, which were presumably attributed to the increase in insulin concentrations in the culture dish, confirming the function of these insulin-sensor-cells. Therefore, we demonstrated that heterogenetic insulin secretion in single-living pancreatic β cells could be measured directly using the insulin sensor cells.
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Affiliation(s)
- Hajime Shigeto
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan. and Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan and Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Takuto Ono
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan. and Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
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12
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Satake S, Shinmori H, Kawabata S, Sugikawa K, Funabashi H, Kuroda A, Ikeda A. High photodynamic activities of water-soluble inclusion complexes of 5,15-diazaporphyrins in cyclodextrin. Org Biomol Chem 2019; 17:3141-3149. [DOI: 10.1039/c9ob00101h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inclusion complexes of 5,15-diazaporphyrin derivatives in trimethyl-β-cyclodextrin exhibited high photodynamic activity under visible-light irradiation at wavelengths greater than 620 nm.
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Affiliation(s)
- Shuhei Satake
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Hideyuki Shinmori
- Division of Medicine and Engineering Science
- Graduate Faculty of Interdisciplinary Research
- Faculty of Life and Environmental Science University of Yamanashi
- Kofu 400-8510
- Japan
| | - Shigeki Kawabata
- Department of Liberal Arts and Sciences
- Faculty of Engineering
- Toyama Prefectural University
- Imizu
- Japan
| | - Kouta Sugikawa
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima 739-8530
- Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima 739-8530
- Japan
| | - Atsushi Ikeda
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
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13
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Nakaya T, Horiguchi B, Hino S, Sugikawa K, Funabashi H, Kuroda A, Ikeda A. Stabilisation of lipid membrane-incorporated porphyrin derivative aqueous solutions and their photodynamic activities. Photochem Photobiol Sci 2019; 18:459-466. [DOI: 10.1039/c8pp00350e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A porphyrin derivative which exists on the hydrophilic surface of the liposomes showed high photodynamic activity.
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Affiliation(s)
- Toshimi Nakaya
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Banri Horiguchi
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Shodai Hino
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Kouta Sugikawa
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Atsushi Ikeda
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
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14
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Motomura K, Sano K, Watanabe S, Kanbara A, Gamal Nasser AH, Ikeda T, Ishida T, Funabashi H, Kuroda A, Hirota R. Synthetic Phosphorus Metabolic Pathway for Biosafety and Contamination Management of Cyanobacterial Cultivation. ACS Synth Biol 2018; 7:2189-2198. [PMID: 30203964 DOI: 10.1021/acssynbio.8b00199] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent progress in genetic engineering and synthetic biology have greatly expanded the production capabilities of cyanobacteria, but concerns regarding biosafety issues and the risk of contamination of cultures in outdoor culture conditions remain to be resolved. With this dual goal in mind, we applied the recently established biological containment strategy based on phosphite (H3PO3, Pt) dependency to the model cyanobacterium Synechococcus elongatus PCC 7942 ( Syn 7942). Pt assimilation capability was conferred on Syn 7942 by the introduction of Pt dehydrogenase (PtxD) and hypophosphite transporter (HtxBCDE) genes that allow the uptake of Pt, but not phosphate (H3PO4, Pi). We then identified and disrupted the two indigenous Pi transporters, pst (Synpcc7942_2441 to 2445) and pit (Synpcc7942_0184). The resultant strain failed to grow on any media containing various types of P compounds other than Pt. The strain did not yield any escape mutants for at least 28 days with a detection limit of 3.6 × 10-11 per colony forming unit, and rapidly lost viability in the absence of Pt. Moreover, growth competition of the Pt-dependent strain with wild-type cyanobacteria revealed that the Pt-dependent strain could dominate in cultures containing Pt as the sole P source. Because Pt is rarely available in aquatic environments this strategy can contribute to both biosafety and contamination management of genetically engineered cyanobacteria.
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Affiliation(s)
- Kei Motomura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kosuke Sano
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Akihiro Kanbara
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Abdel-Hady Gamal Nasser
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency (JST-ALCA), Chiyoda-ku, Tokyo 102-0076, Japan
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15
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Antoku D, Satake S, Mae T, Sugikawa K, Funabashi H, Kuroda A, Ikeda A. Cover Feature: Improvement of Photodynamic Activity of Lipid–Membrane‐Incorporated Fullerene Derivative by Combination with a Photo‐Antenna Molecule (Chem. Eur. J. 29/2018). Chemistry 2018. [DOI: 10.1002/chem.201801526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daiki Antoku
- Department of Applied Chemistry, Graduate School of EngineeringHiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima 739-8527 Japan
| | - Shuhei Satake
- Department of Applied Chemistry, Graduate School of EngineeringHiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima 739-8527 Japan
| | - Tomoya Mae
- Department of Applied Chemistry, Graduate School of EngineeringHiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima 739-8527 Japan
| | - Kouta Sugikawa
- Department of Applied Chemistry, Graduate School of EngineeringHiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima 739-8527 Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of MatterHiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8530 Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of MatterHiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8530 Japan
| | - Atsushi Ikeda
- Department of Applied Chemistry, Graduate School of EngineeringHiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima 739-8527 Japan
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16
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Antoku D, Satake S, Mae T, Sugikawa K, Funabashi H, Kuroda A, Ikeda A. Improvement of Photodynamic Activity of Lipid-Membrane-Incorporated Fullerene Derivative by Combination with a Photo-Antenna Molecule. Chemistry 2018. [PMID: 29512833 DOI: 10.1002/chem.201800674] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The weak absorbance of pristine C60 , C70 , and fullerene derivatives at wavelengths over 600 nm hampers the use of these molecules as photosensitizers (PSs) for photodynamic therapy (PDT). The coexistence of light-harvesting antenna molecules with a fullerene derivative in lipid membrane bilayers solved this issue. By controlling the location of the C60 derivative in the lipid membrane, the liposomal dyad system for PDT improved the photodynamic activity via an efficient photoenergy transfer from antenna molecules to the fullerene derivative. The photodynamic activity was found to be much higher than those of dyad systems using pristine C60 and C70 .
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Affiliation(s)
- Daiki Antoku
- Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, 739-8527, Japan
| | - Shuhei Satake
- Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, 739-8527, Japan
| | - Tomoya Mae
- Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, 739-8527, Japan
| | - Kouta Sugikawa
- Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, 739-8527, Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan
| | - Atsushi Ikeda
- Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, 739-8527, Japan
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17
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Nakatsuka K, Shigeto H, Kuroda A, Funabashi H. Corrigendum to “A split G-quadruplex-based DNA nano-tweezers structure as a signal-transducing molecule for the homogeneous detection of specific nucleic acids” [Biosens. Bioelectron. 74 (2015) 222–226]. Biosens Bioelectron 2017; 94:729. [DOI: 10.1016/j.bios.2017.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Ikeda A, Satake S, Mae T, Ueda M, Sugikawa K, Shigeto H, Funabashi H, Kuroda A. Photodynamic Activities of Porphyrin Derivative-Cyclodextrin Complexes by Photoirradiation. ACS Med Chem Lett 2017; 8:555-559. [PMID: 28523110 DOI: 10.1021/acsmedchemlett.7b00098] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
Water-soluble cyclodextrin (CyD) complexed with porphyrin derivatives with different substituents in the meso-positions showed different photodynamic activities toward cancer cells under illumination at wavelengths over 600 nm, the most suitable wavelengths for photodynamic therapy (PDT). In particular, aniline- and phenol-substituted derivatives had high photodynamic activity because of the efficient intracellular uptake of the complexes by tumor cells. These complexes showed greater photodynamic activity than photofrin, currently the main drug in clinical use as a photosensitizer. These results represent a significant step toward the optimization of porphyrin derivatives as photosensitizers.
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Affiliation(s)
- Atsushi Ikeda
- Department
of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Shuhei Satake
- Department
of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Tomoya Mae
- Department
of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Masafumi Ueda
- Department
of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Kouta Sugikawa
- Department
of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Hajime Shigeto
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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19
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Takayama K, Sasabe N, Hotta S, Yokonuma K, Funabashi H, Kumagai T. Detection of oral bacterial flora using DNA array. Dent Mater 2017. [DOI: 10.1016/j.dental.2017.08.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Ikeda A, Mae T, Ueda M, Sugikawa K, Shigeto H, Funabashi H, Kuroda A, Akiyama M. Improved photodynamic activities of liposome-incorporated [60]fullerene derivatives bearing a polar group. Chem Commun (Camb) 2017; 53:2966-2969. [DOI: 10.1039/c7cc00302a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A liposome-incorporated C60 derivative bearing a polar group showed higher photodynamic activity than the system incorporating pristine C60 because of its high 1O2 generation ability, as well as its localization in the liposomes.
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Affiliation(s)
- Atsushi Ikeda
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Tomoya Mae
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Masafumi Ueda
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Kouta Sugikawa
- Department of Applied Chemistry
- Graduate School of Engineering
- Hiroshima University
- Higashi-Hiroshima 739-8527
- Japan
| | - Hajime Shigeto
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Hisakage Funabashi
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology
- Graduate School of Advanced Sciences of Matter
- Hiroshima University
- Higashi-Hiroshima
- Japan
| | - Motofusa Akiyama
- Faculty of Science and Engineering
- Chuo University
- Tokyo 113-8551
- Japan
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21
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Shigeto H, Nakatsuka K, Ikeda T, Hirota R, Kuroda A, Funabashi H. Continuous Monitoring of Specific mRNA Expression Responses with a Fluorescence Resonance Energy Transfer-Based DNA Nano-tweezer Technique That Does Not Require Gene Recombination. Anal Chem 2016; 88:7894-8. [DOI: 10.1021/acs.analchem.6b02710] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hajime Shigeto
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Keisuke Nakatsuka
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
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22
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Nakatsuka K, Shigeto H, Kuroda A, Funabashi H. A split G-quadruplex-based DNA nano-tweezers structure as a signal-transducing molecule for the homogeneous detection of specific nucleic acids. Biosens Bioelectron 2015; 74:222-6. [DOI: 10.1016/j.bios.2015.06.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/12/2015] [Accepted: 06/23/2015] [Indexed: 12/23/2022]
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23
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Abstract
A DNA nano-tweezer (DNA-NT) structure-based target mRNA detection probe, which uses fluorescence resonance energy transfer (FRET) as a detection signal and works as a single molecule, has been developed. This FRET-paired fluorescent dye-modified DNA-NT, self-assembled from three single-stranded DNAs, alters its structure from open to closed states and produces a FRET signal in response to in vitro transcripts of Hes-1 mRNA. Our results showed that the FRET-based DNA-NT detected both GLUT1 mRNA as a pre-fixed target mRNA model and Hes-1 mRNA as a model expressed inside a living cell. These results confirm the feasibility of using the FRET-based DNA-NT for imaging analysis of target mRNA.
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Affiliation(s)
- Hisakage Funabashi
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan.
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24
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Shigeto H, Ikeda T, Kuroda A, Funabashi H. A BRET-based homogeneous insulin assay using interacting domains in the primary binding site of the insulin receptor. Anal Chem 2015; 87:2764-70. [PMID: 25655236 DOI: 10.1021/ac504063x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new homogeneous insulin assay requiring no chemical modification of an insulin recognition domain, which can be applied to continuous monitoring of the time-dependent cellular response in vitro, was developed. The carboxy-terminal α-chain (αCT) segment and first leucine-rich-repeat (L1) domain in the primary binding site on the insulin receptor were genetically fused with a bioluminescent protein (Nanoluc, Nluc) and a fluorescent protein (yellow fluorescent protein, YPet) to produce the insulin-sensing probe proteins Nluc-αCT and L1-YPet. The BRET signal was observed on simple mixing of insulin with these protein probes, in a so-called homogeneous assay. The BRET signal was proportional to the insulin concentration, and the lower detection limit was 0.8 μM. Time-dependent insulin secretion from drug-stimulated MIN6 cells was also successfully monitored continuously with the probe proteins. This BRET-based homogeneous insulin assay method is thus expected to be applicable to drug development by high-throughput screening.
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Affiliation(s)
- Hajime Shigeto
- Institute for Sustainable Sciences and Development, Hiroshima University , Higashihiroshima, Hiroshima 739-8511, Japan
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Ikeda A, Hino S, Mae T, Tsuchiya Y, Sugikawa K, Tsukamoto M, Yasuhara K, Shigeto H, Funabashi H, Kuroda A, Akiyama M. Porphyrin-uptake in liposomes and living cells using an exchange method with cyclodextrin. RSC Adv 2015. [DOI: 10.1039/c5ra24985f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A preparation of a lipid-membrane-incorporated tetraphenylporphyrin was achieved from the corresponding tetraphenylporphyrin·cyclodextrin complexes using an exchange method in both liposomes and cells.
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Funabashi H, Yanagi S, Suzuki S, Mie M, Kobatake E. Assembly of zinc finger motif-fused enzymes on a dsDNA scaffold for catalyzing consecutive reactions with a proximity effect. Biotechnol Lett 2014; 37:109-14. [PMID: 25216646 DOI: 10.1007/s10529-014-1644-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/14/2014] [Indexed: 11/25/2022]
Abstract
The feasibility of assembling enzymes, catalyzing consecutive reactions, on to a double-stranded DNA (dsDNA) scaffold utilizing zinc finger motifs is described. The catalytic activities of two zinc finger motif-fused enzymes catalyzing a bioluminescence reaction with energy recycling, namely pyruvate phosphate dikinase and firefly luciferase, have been evaluated. Bioluminescence measurements with dsDNA scaffolds coding a different distance between the binding sites for each zinc finger motif-fused enzyme confirmed the effect of the distance, proving the proximity effect of ATP recycling presumed to be the result of efficient intermediate diffusion. Thus, fusion to zinc finger motifs offers a promising option for the assembly of bi-enzymes, catalyzing a consecutive reaction, onto a dsDNA scaffold with a proximity effect.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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Tran TNN, Cui J, Hartman MR, Peng S, Funabashi H, Duan F, Yang D, March JC, Lis JT, Cui H, Luo D. A universal DNA-based protein detection system. J Am Chem Soc 2013; 135:14008-11. [PMID: 23978265 DOI: 10.1021/ja405872g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.
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Affiliation(s)
- Thua N N Tran
- Department of Biological & Environmental Engineering, ∥Department of Molecular Biology and Genetics, and ⊥Kavli Institute at Cornell for Nanoscale Science, Cornell University , Ithaca, New York 14853, United States
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28
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Saito M, Kakutani Y, Kaburagi M, Funabashi H, Matsuoka H. Development of a protocol for selection of genes fit for the in vivo knockdown method and its application to insulin receptor substrate genes in mice. Exp Anim 2013; 62:117-25. [PMID: 23615306 DOI: 10.1538/expanim.62.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Prediabetes model mice in which more than one gene associated with diabetes is knocked down simultaneously are potentially useful for pharmaceutical and medical studies of diabetes. However, the effective conditions for sufficient knockdown in vivo are dependent on the intrinsic properties of the target genes. It is necessary to investigate which genes are applicable or not to the in vivo knockdown method. In this study, insulin receptor substrate 1 and 2 (Irs-1, Irs-2) were selected as target genes. Effective siRNAs against the respective genes were designed, and their efficacy was confirmed by cell-based experiments. Based on the results of siRNAs, shRNA expression vectors against Irs-1 and Irs-2 were constructed, respectively. Their efficacy was also confirmed by cell-based experiments. A hydrodynamic method was applied to the delivery of the vectors to mice. This method was found to be effective for predominant delivery to the liver by demonstrative delivery of an EGFP expression vector and successive histochemical analysis. Fifty micrograms of the shRNA expression vector was injected into the tail vein. After 24 h, the liver, pancreas, and muscle were isolated, and the expression levels of Irs-1 and Irs-2 were analyzed by quantitative RT-PCR. In the liver, Irs-2 was effectively knocked down to 60% of the control level, but Irs-1 was not influenced even under the same conditions. The protocol developed here is feasible for the selection of genes fit for in vivo knockdown method.
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Affiliation(s)
- Mikako Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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29
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Funabashi H, Oura S, Saito M, Matsuoka H. Targeted delivery of a decoy oligodeoxynucleotide to a single ES cell by femtoinjection. Nanomedicine 2013; 9:855-63. [PMID: 23506950 DOI: 10.1016/j.nano.2013.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 01/26/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
Abstract
UNLABELLED Femtoinjection has been proposed as a feasible approach for the targeted delivery of a decoy oligodeoxynucleotide (ODN) into a single ES cell for the study of transcription factor activity. Here, we evaluated the utility of decoy ODN delivery via femtoinjection in an ES cell model in which Venus fluorescent protein was expressed under the control of the tet-off system. Femtoinjection of a control decoy (Con-decoy) and a tetracycline response element decoy (TRE-decoy) into the cytoplasm had no apparent effect on Venus fluorescent protein expression; however, femtoinjection of the TRE-decoy into the nucleus successfully suppressed expression of the Venus fluorescent protein. We therefore conclude that it is feasible to suppress the activity of a transcription factor in a single ES cell by the delivery of a decoy ODN into the nucleus using the femtoinjection technique. FROM THE CLINICAL EDITOR The authors of this novel basic science study successfully demonstrate a femtoinjection technique to deliver a decoy oligodeoxynucleotide into a single ES cell.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16, Naka-cho, Koganei, Tokyo, Japan
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30
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Lee JB, Peng S, Yang D, Roh YH, Funabashi H, Park N, Rice EJ, Chen L, Long R, Wu M, Luo D. A mechanical metamaterial made from a DNA hydrogel. Nat Nanotechnol 2012; 7:816-820. [PMID: 23202472 DOI: 10.1038/nnano.2012.211] [Citation(s) in RCA: 366] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/31/2012] [Indexed: 05/18/2023]
Abstract
Metamaterials are artificial substances that are structurally engineered to have properties not typically found in nature. To date, almost all metamaterials have been made from inorganic materials such as silicon and copper, which have unusual electromagnetic or acoustic properties that allow them to be used, for example, as invisible cloaks, superlenses or super absorbers for sound. Here, we show that metamaterials with unusual mechanical properties can be prepared using DNA as a building block. We used a polymerase enzyme to elongate DNA chains and weave them non-covalently into a hydrogel. The resulting material, which we term a meta-hydrogel, has liquid-like properties when taken out of water and solid-like properties when in water. Moreover, upon the addition of water, and after complete deformation, the hydrogel can be made to return to its original shape. The meta-hydrogel has a hierarchical internal structure and, as an example of its potential applications, we use it to create an electric circuit that uses water as a switch.
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Affiliation(s)
- Jong Bum Lee
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
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31
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Matsuba Y, Sasaki N, Tera M, Okamura M, Abe Y, Okamoto E, Nakamura H, Funabashi H, Takatsu M, Saito M, Matsuoka H, Nagasawa K, Ozeki Y. A Novel Glucosylation Reaction on Anthocyanins Catalyzed by Acyl-Glucose–Dependent Glucosyltransferase in the Petals of Carnation and Delphinium. The Plant Cell 2010; 22:3374-89. [PMID: 20971893 PMCID: PMC2990145 DOI: 10.1105/tpc.110.077487] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Abstract
Glucosylation of anthocyanin in carnations (Dianthus caryophyllus) and delphiniums (Delphinium grandiflorum) involves novel sugar donors, aromatic acyl-glucoses, in a reaction catalyzed by the enzymes acyl-glucose–dependent anthocyanin 5(7)-O-glucosyltransferase (AA5GT and AA7GT). The AA5GT enzyme was purified from carnation petals, and cDNAs encoding carnation Dc AA5GT and the delphinium homolog Dg AA7GT were isolated. Recombinant Dc AA5GT and Dg AA7GT proteins showed AA5GT and AA7GT activities in vitro. Although expression of Dc AA5GT in developing carnation petals was highest at early stages, AA5GT activity and anthocyanin accumulation continued to increase during later stages. Neither Dc AA5GT expression nor AA5GT activity was observed in the petals of mutant carnations; these petals accumulated anthocyanin lacking the glucosyl moiety at the 5 position. Transient expression of Dc AA5GT in petal cells of mutant carnations is expected to result in the transfer of a glucose moiety to the 5 position of anthocyanin. The amino acid sequences of Dc AA5GT and Dg AA7GT showed high similarity to glycoside hydrolase family 1 proteins, which typically act as β-glycosidases. A phylogenetic analysis of the amino acid sequences suggested that other plant species are likely to have similar acyl-glucose–dependent glucosyltransferases.
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Affiliation(s)
- Yuki Matsuba
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Nobuhiro Sasaki
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Masachika Okamura
- Central Laboratories for Frontier Technology, Kirin Holdings Company, Tochigi 329-1414, Japan
| | - Yutaka Abe
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Emi Okamoto
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Haruka Nakamura
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Hisakage Funabashi
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Makoto Takatsu
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Mikako Saito
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Hideaki Matsuoka
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Yoshihiro Ozeki
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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32
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Nishikawa M, Mizuno Y, Mohri K, Matsuoka N, Rattanakiat S, Takahashi Y, Funabashi H, Luo D, Takakura Y. Biodegradable CpG DNA hydrogels for sustained delivery of doxorubicin and immunostimulatory signals in tumor-bearing mice. Biomaterials 2010; 32:488-94. [PMID: 20932569 DOI: 10.1016/j.biomaterials.2010.09.013] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 09/06/2010] [Indexed: 01/07/2023]
Abstract
Immunostimulatory CpG DNA was self-assembled to form DNA hydrogels for use as a sustained delivery system for both intercalated doxorubicin (DXR) and immunostimulatory CpG motifs for cancer treatment. X-shaped DNA (X-DNA) was designed as a building unit, and underwent ligation to form DNA hydrogels. Two types of X-DNA were constructed using four oligodeoxynucleotides each, one containing six potent CpG motifs (CpG X-DNA) and the other with none (CpG-free X-DNA). CpG X-DNA was more effective than its components or the CpG-free counterpart in terms of the production of tumor necrosis factor-α from murine macrophage-like RAW264.7 cells, as well as maturation of the murine dendritic DC2.4 cells. The cytotoxic effects of X-DNA, DXR and their complexes were examined in a co-culture system of colon26/Luc cells, a murine adenocarcinoma clone stably expressing firefly luciferase, and RAW264.7 cells. DXR/CpG X-DNA showed the highest ability to inhibit the proliferation of colon26/Luc cells. DXR was slowly released from CpG DNA hydrogels. Injections of DXR/CpG DNA hydrogels into a subcutaneous colon26 tumor effectively inhibited tumor growth. These results show that CpG DNA hydrogels are an effective sustained system for delivery of immunostimulatory signals to TLR9-positive immune cells and DXR to cancer cells.
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Affiliation(s)
- Makiya Nishikawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
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Funabashi H, Takatsu M, Saito M, Matsuoka H. Sox2 regulatory region 2 sequence works as a DNA nuclear targeting sequence enhancing the efficiency of an exogenous gene expression in ES cells. Biochem Biophys Res Commun 2010; 400:554-8. [DOI: 10.1016/j.bbrc.2010.08.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Accepted: 08/25/2010] [Indexed: 01/01/2023]
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Lee JB, Roh YH, Um SH, Funabashi H, Cheng W, Cha JJ, Kiatwuthinon P, Muller DA, Luo D. Multifunctional nanoarchitectures from DNA-based ABC monomers. Nat Nanotechnol 2009; 4:430-6. [PMID: 19581895 PMCID: PMC7097395 DOI: 10.1038/nnano.2009.93] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 03/25/2009] [Indexed: 05/18/2023]
Abstract
The ability to attach different functional moieties to a molecular building block could lead to applications in nanoelectronics, nanophotonics, intelligent sensing and drug delivery. The building unit needs to be both multivalent and anisotropic, and although many anisotropic building blocks have been created, these have not been universally applicable. Recently, DNA has been used to generate various nanostructures or hybrid systems, and as a generic building block for various applications. Here, we report the creation of anisotropic, branched and crosslinkable building blocks (ABC monomers) from which multifunctional nanoarchitectures have been assembled. In particular, we demonstrate a target-driven polymerization process in which polymers are generated only in the presence of a specific DNA molecule, leading to highly sensitive pathogen detection. Using this monomer system, we have also designed a biocompatible nanovector that delivers both drugs and tracers simultaneously. Our approach provides a general yet versatile route towards the creation of a range of multifunctional nanoarchitectures.
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Affiliation(s)
- Jong B. Lee
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
| | - Young H. Roh
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
| | - Soong Ho Um
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
- Present Address: Present address: Department of Materials Science and Engineering, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA,
| | - Hisakage Funabashi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
| | - Wenlong Cheng
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
| | - Judy J. Cha
- Department of Applied and Engineering Physics, Cornell University, Ithaca, 14850 New York USA
| | - Pichamon Kiatwuthinon
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
| | - David A. Muller
- Department of Applied and Engineering Physics, Cornell University, Ithaca, 14850 New York USA
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, 14850 New York USA
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Abstract
Proteins are important biomaterials and are generally produced in living cells. Here, we show a novel DNA hydrogel that is capable of producing functional proteins without any living cells. This protein-producing gel (termed 'the P-gel system' or 'P-gel') consists of genes as part of the gel scaffolding. This is the first time that a hydrogel has been used to produce proteins. The efficiency was about 300 times higher than current, solution-based systems. In terms of volumetric yield, the P-gel produced up to 5 mg ml(-1) of functional proteins. The mechanisms behind the high efficiency and yield include improved gene stability, higher local concentration and a faster enzyme turnover rate due to a closer proximity of genes. We have tested a total of 16 different P-gels and have successfully produced all 16 proteins including membrane and toxic proteins, demonstrating that the P-gel system can serve as a general protein production technology.
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Affiliation(s)
- Nokyoung Park
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853-5701, USA
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36
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Smith J, Gao B, Funabashi H, Tran TN, Luo D, Ahner BA, Steenhuis TS, Hay AG, Walter MT. Pore-scale quantification of colloid transport in saturated porous media. Environ Sci Technol 2008; 42:517-523. [PMID: 18284156 DOI: 10.1021/es070736x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
It is currently not clear how to quantifiably relate pore-scale observations of colloid transportto larger scales, so,we proposed a geometric theory showing that pore-scale-derived rate constants may be appropriate to model a larger scale system. This study considered three different types of colloids: latex microspheres, Escherichia coli, and microspheres made of poly lactic acid (PLA). Colloid attachment and detachment rate constants were calculated using digital microscope images, taken in rapid (1 s) sequences, from which rates of attaching and detaching colloids were readily observed. Average rate constants from >1000 images per colloid-type were used to model Darcy-scale colloid transport breakthrough curves. The modeled and observed breakthrough curves agreed well for all three types of colloids. However, for latex and PLA microspheres, the model systematically under predicted the breakthrough curves' rising limb, which may indicate that the rate "constants" are actually dependent on the amount of attached colloids. Insights into these sorts of complexities are best addressed by research that considers both pore-scale phenomena and larger-scale transport responses.
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Affiliation(s)
- Jennifer Smith
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
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Abstract
It is widely recognized that stimuli-responsive nanostructures play a promising role in nanodevices for medical treatments and experimental tools. We have designed and constructed a basic structure which controls the distance between two termini domains through temperature reversibility. Our structure, shaped like a bouquet, is composed of two proteins, alpha-helix and elastin-like protein (ELP). Alpha-helices align and bundle the ELP while ELP twists and forms a fiber-like structure at warm temperatures. This ELP conformational change alters the distance between the structure termini at the site opposite the alpha-helix. We connected enhanced yellow fluorescent protein (EYFP) and enhanced cyan fluorescent protein (ECFP) at the structure's two termini to evaluate the distance using fluorescence resonance energy transfer (FRET) efficiency. These proteins spontaneously formed a complex which decreased the distance between the two fluorescent proteins located at its termini, at physiologically relevant temperatures. This change was repeated with complete reversibility (n = 5).
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Affiliation(s)
- Yoshihiko Fujita
- Department of Biological Information Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Endoh T, Funabashi H, Mie M, Kobatake E. Method for detection of specific nucleic acids by recombinant protein with fluorescent resonance energy transfer. Anal Chem 2007; 77:4308-14. [PMID: 16013840 DOI: 10.1021/ac048491j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Detection of specific nucleic acids is important to understand cellular mechanisms and functions of gene regulation. Here, we demonstrated a novel method to detect specific nucleic acids using recombinant protein and oligonucleotides. A recombinant protein YRGnC-11ad, which has a Rev-peptide between enhanced yellow fluorescent protein (EYFP) and enhanced cyan fluorescent protein (ECFP) was constructed and expressed in HeLa cells. Rev-peptide, which corresponds to amino acids 34-50 of the HIV-1 Rev protein, indicates disordered structure in solution but forms alpha-helical and elongated conformation upon binding to Rev response element RNA (RRE-RNA) and Rev-aptamer, respectively. We confirmed that YRGnC-11ad could specifically bind to RRE-RNA and Rev-aptamer in cell lysate, and fluorescent resonance energy transfer (FRET) signal was changed upon binding following the conformational change of Rev-peptide. To utilize this FRET signal change toward the detection of specific nucleic acids, we split the RRE-RNA sequence and connected to the complementary oligonucleotide for target nucleic acids. When each two oligonucleotides hybridized to an adjacent region of target nucleic acids correctly, a Rev-peptide binding site was reformed on the hybridized complex. And we could confirm that YRGnC-11ad recombinant protein indicated FRET increase upon binding to the hybridized complex in cell lysate. These results suggest that the recombinant protein probe is available for specific nucleic acid detection.
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Affiliation(s)
- Tamaki Endoh
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama, 226-8501, Japan
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Endoh T, Mie M, Funabashi H, Sawasaki T, Endo Y, Kobatake E. Construction of intramolecular luciferase complementation probe for detecting specific RNA. Bioconjug Chem 2007; 18:956-62. [PMID: 17367182 DOI: 10.1021/bc060351o] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intermolecular enzyme complementation assay is a useful method for detecting protein-protein interactions. Specifically, bioluminescent signals produced from reconstructed split luciferase fragments are powerful tools for in vivo analysis because the bioluminescent signals have been visualized both in cultured cells and living animals. However, they are limited for detection and evaluation of biological events relevant to intermolecular protein-protein interactions. In this study, we constructed an intramolecular luciferase complementation probe for detecting target biomolecules other than protein-protein interactions. It consists of peptide-inserted firefly luciferase (PI-FLuc) containing a short peptide between internally divided firefly luciferase. The inserted short peptide triggers FLuc complementation or discomplementation and subsequent reactivation or inactivation of FLuc activity through its induced fit conformational changes. We chose RNA binding arginine rich motif (ARM) peptides, Rev and/or Tat, for model peptide insertion, and expressed constructed PI-FLuc probe variants using a wheat germ cell-free protein synthesis system. They showed FLuc activity changes, reactivation, or inactivation after binding to their specific RNA targets. Furthermore, to expand the versatility of the PI-FLuc RNA detection system, we designed split-RNA probes built to reform the ARM peptide binding site in the presence of arbitrarily selected target-RNA. As a result, the target RNA was homogeneously detected by FLuc luminescent signals mediated by a cooperative function of the PI-FLuc and split-RNA probe sets.
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Affiliation(s)
- Tamaki Endoh
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, 4259, Nagatsuta, Yokohama, 226-8501, Japan
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Funabashi H, Ubukata M, Ebihara T, Aizawa M, Mie M, Kobatake E. Assessment of small ligand-protein interactions by electrophoretic mobility shift assay using DNA-modified ligand as a sensing probe. Biotechnol Lett 2007; 29:785-9. [PMID: 17279446 DOI: 10.1007/s10529-006-9301-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/18/2006] [Accepted: 12/21/2006] [Indexed: 11/29/2022]
Abstract
The interaction between a small ligand and a protein were assessed by electrophoretic mobility shift assay. A sensing probe was created by modifying the model ligand, biotin, with DNA. The complex of DNA-modified ligand and anti-biotin antibody or streptavidin as a target protein was analyzed by agarose gel electrophoresis. The band corresponding to the DNA-modified ligand was shifted in the presence of the target protein, and the intensities of the shifted bands were decreased by adding increasing concentrations of free ligand ranging from 0.1 microM to 100 microM. From this calibration the concentration of ligand in the samples could be determined, allowing for evaluation of the interaction between a small ligand and its target.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama , 226-8501, Japan
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41
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Noda T, Kawamura R, Funabashi H, Mie M, Kobatake E. Transduction of NeuroD2 protein induced neural cell differentiation. J Biotechnol 2006; 126:230-6. [PMID: 16730830 DOI: 10.1016/j.jbiotec.2006.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 03/28/2006] [Accepted: 04/07/2006] [Indexed: 12/31/2022]
Abstract
NeuroD2, one of the neurospecific basic helix-loop-helix transcription factors, has the ability to induce neural differentiation in undifferentiated cells. In this paper, we show that transduction of NeuroD2 protein induced mouse neuroblastoma cell line N1E-115 into neural differentiation. NeuroD2 has two basic-rich domains, one is nuclear localization signal (NLS) and the other is basic region of basic helix-loop-helix (basic). We constructed some mutants of NeuroD2, ND2(Delta100-115) (lack of NLS), ND2(Delta123-134) (lack of basic) and ND2(Delta100-134) (lack of both NLS and basic) for transduction experiments. Using these proteins, we have shown that NLS region of NeuroD2 plays a role of protein transduction. Continuous addition of NeuroD2 protein resulted in N1E-115 cells adopting neural morphology after 4 days and Tau mRNA expression was increased. These results suggest that neural differentiation can be induced by direct addition of NeuroD2 protein.
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Affiliation(s)
- Tomohide Noda
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatuta, Yokohama, Kanagawa 226-8501, Japan
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Mitsuyama K, Matsumoto S, Rose-John S, Suzuki A, Hara T, Tomiyasu N, Handa K, Tsuruta O, Funabashi H, Scheller J, Toyonaga A, Sata M. STAT3 activation via interleukin 6 trans-signalling contributes to ileitis in SAMP1/Yit mice. Gut 2006; 55:1263-9. [PMID: 16682432 PMCID: PMC1860050 DOI: 10.1136/gut.2005.079343] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIMS SAMP1/Yit mice spontaneously develops intestinal inflammation. Previously, we demonstrated that the signal transducer and activator of transcription (STAT)-3/suppressor of cytokine signalling (SOCS)-3 pathway is pivotal in human inflammatory bowel disease. In our studies in SAMP1/Yit mice, the aim was to investigate whether STAT3 activation contributes to ileitis and to examine the therapeutic effects of this signal blockade. METHODS Intestinal expression of phospho-STAT3 in SAMP1/Yit mice and control AKR/J mice was examined by western blotting and immunohistochemistry. SOCS3 and interleukin 6 (IL-6) mRNA were determined by northern blotting and reverse transcription-polymerase chain reaction, respectively. We also examined the effects of intravenously injected hyper-IL-6, an IL-6/soluble IL-6 receptor fusion protein, and of soluble gp130-Fc, a specific inhibitor of soluble IL-6 receptor signalling, on STAT3 phosphorylation and disease severity in SAMP1/Yit mice. RESULTS Phospho-STAT3 was expressed strongly during the disease course in SAMP1/Yit mice but only transiently in AKR/J mice. Phospho-STAT3 was localised to epithelial and mononuclear cells in the diseased intestine of SAMP1/Yit mice. SOCS3 as well as IL-6 mRNAs were expressed in affected intestine. Administration of hyper-IL-6 caused disease exacerbation and enhancement of STAT3 phosphorylation. In contrast, soluble gp130-Fc administration ameliorated the disease and suppressed STAT3 phosphorylation. CONCLUSION STAT3 signalling is critical in the development of intestinal inflammation in SAMP1/Yit mice. Blockade of this signalling pathway by soluble gp130-Fc may have therapeutic effects in inflammatory bowel disease.
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Affiliation(s)
- K Mitsuyama
- Second Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan.
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Mie M, Mori K, Funabashi H, Kobatake E. Delivery of antibody-captured proteins into living cells using PTD-fused protein A. Biotechnol Lett 2006; 28:1209-14. [PMID: 16804765 DOI: 10.1007/s10529-006-9076-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 04/12/2006] [Indexed: 10/24/2022]
Abstract
Protein transduction domain (PTD)-mediated protein delivery into animal cells is a useful technique for regulating cellular functions. Proteins captured by antibodies were delivered into living cells using an antibody/PTD-fused protein A complex. As a model protein, fluorescent-modified antibodies, captured by their respective primary antibody, were analyzed by fluorescence-activated cell sorting (FACS) which showed that the fluorescent-modified antibodies were directly delivered into cells. Peroxidase, captured by its specific antibody, was also delivered into cells and retained its activity.
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Affiliation(s)
- Masayasu Mie
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
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Elloumi I, Kobayashi R, Funabashi H, Mie M, Kobatake E. Construction of epidermal growth factor fusion protein with cell adhesive activity. Biomaterials 2006; 27:3451-8. [PMID: 16497372 DOI: 10.1016/j.biomaterials.2006.02.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 02/02/2006] [Indexed: 11/30/2022]
Abstract
A novel protein for controlling cellular functions was constructed by combining functional units of various proteins. The Arg-Gly-Asp (RGD) sequence functioning as a cell adhesive function, an epidermal growth factor (EGF) as a cell growth function, and a hydrophobic sequence (E12) as an efficient assembling function, were combined and incorporated into one molecule. The fusion protein, designated ERE-EGF, was produced in Escherichia coli and purified with affinity chromatography using a His-tag. The ERE-EGF coated on an unmodified hydrophobic surface of a cell-culture plate (through the hydrophobic E12 moiety) retained both cell adhesive activity (through the RGD sequence) and cell growth activity (through the EGF moiety).
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Affiliation(s)
- Imen Elloumi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Ihara H, Mie M, Funabashi H, Takahashi F, Sawasaki T, Endo Y, Kobatake E. In vitro selection of zinc finger DNA-binding proteins through ribosome display. Biochem Biophys Res Commun 2006; 345:1149-54. [PMID: 16714002 DOI: 10.1016/j.bbrc.2006.05.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 05/02/2006] [Indexed: 11/23/2022]
Abstract
DNA-binding proteins with sequence specificities have a variety of applications. To create novel functional DNA-binding proteins, in vivo selection methods have been developed. There are, however, crucial problems with such methods, e.g., limitation of library size and difficulty of expression of toxic proteins for the host cells. In order to overcome these problems, we developed a novel way to select DNA-binding proteins using an in vitro ribosome display technique. The three zinc finger DNA-binding protein libraries, based on a Zif268 containing randomized sequence in each finger, were prepared and transcribed to mRNA in vitro. The ternary ribosomal complexes, formed by mRNA, ribosome, and translated DNA-binding protein during translation in a rabbit reticulocyte in vitro translation system, were selected with biotinylated target DNA fragments bound to streptavidin magnetic beads. The extracted mRNAs from the selected complexes were amplified using reverse transcription PCR and then sequenced. This is the first report of the selection of DNA-binding proteins involving an in vitro ribosome display technique.
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Affiliation(s)
- Hiroshi Ihara
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Nakamura M, Mie M, Funabashi H, Yamamoto K, Ando J, Kobatake E. Cell-surface-localized ATP detection with immobilized firefly luciferase. Anal Biochem 2006; 352:61-7. [PMID: 16564487 DOI: 10.1016/j.ab.2006.02.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 02/17/2006] [Indexed: 10/24/2022]
Abstract
We demonstrate the application of an assay technique for the detection of ATP efflux from the cell surface. Until recently, the firefly luciferase assay has conventionally been used to detect ATP release because of its high sensitivity and wide detection ability. However, since this technique can be used only to infer the amount of diffused ATP in bulk solutions, it does not accurately reflect the dynamic ATP flux at the cell membrane. We therefore constructed luciferase fusion proteins that could be immobilized onto the cell surface. However, the low activities and limited application ranges of these proteins prompted us to use biotinylated luciferase given its attributes of strong and stable localization. Furthermore, luciferase can be immobilized strongly onto the biotinylated cell surface via streptavidin-biotin binding and can thus be used to determine the dynamic release of ATP near the cell surface.
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Affiliation(s)
- Makiko Nakamura
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Funabashi H, Tanaka Y, Imamura Y, Mie M, Manabe T, Tanaka H, Takahashi T, Handa H, Aizawa M, Kobatake E. Glucose oxidase assisted homogeneous electrochemical receptor binding assay for drug screening. Biosens Bioelectron 2006; 21:1675-83. [PMID: 16169211 DOI: 10.1016/j.bios.2005.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2005] [Revised: 07/23/2005] [Accepted: 08/02/2005] [Indexed: 11/15/2022]
Abstract
Although the idea of homogeneous electrochemical immunoassay using antibody and an electroactive modified antigen as a probe looks to be very useful for high-throughput drug screening, there have been few reports. One reason for this is the difficulty experienced making an electroactive probe, because the introduction of electroactive compounds to antigens often interferes with the antigen-antibody interaction. To apply a homogeneous electrochemical assay to drug screening, we have designed new probes referring to the information of immobilization on beads which could identify the drug receptor. FK506 (also called Tacrolimus), immunosuppressive agent is modified with ferrocene derivatives as an electron mediator between glucose oxidase and an electrode, at a non-obstructing part. One of the probes still indicated the electrochemical activity as a mediator and had the specific binding capability for FKBP12 (FK506 binding protein). The current decrease in response to the additional FKBP12, detected with constant voltage amperometry using the probe, was observed within 5 min. Then, free FK506 as a leader drug, rapamycin and cyclosporine A as unknown drugs were used as a model for drug screening. Since the order of response currents at the same concentration of each drug reflected their binding constants, it was shown that binding capacity of an unknown drug candidate could be estimated by comparison of response currents between the leader drug and the unknown drug candidate. Thus, this glucose oxidase assisted homogeneous electrochemical drug-receptor binding assay has been proved to be a useful tool for drug screening.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Tanaka G, Funabashi H, Mie M, Kobatake E. Fabrication of an antibody microwell array with self-adhering antibody binding protein. Anal Biochem 2006; 350:298-303. [PMID: 16455038 DOI: 10.1016/j.ab.2005.12.034] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Revised: 12/20/2005] [Accepted: 12/26/2005] [Indexed: 11/29/2022]
Abstract
One of the promising methods of preparing antibody arrays is immobilizing antibodies with protein A or protein G, each of which binds specifically to the heavy chain constant (Fc) region of immunoglobulin G (IgG). In this system, antibody immobilization efficiency depends on the number of active Fc binding proteins that need to be immobilized on the surface. Here we have designed and constructed an Fc binding protein with a self-adhering ability that can be immobilized on the hydrophobic surface by simple adsorption. It consists of an Fc binding domain of protein G (G3) and hydrophobic domain of elastin (E72). Direct observation revealed its self-adhering ability on the hydrophobic surface. The enzyme-linked immunosorbent assay (ELISA) showed that it retained antibody binding ability on the surface. The antibody array model was prepared on a hydrophobic microwell glass slide with E72G3, which specifically detect the antigen with a sevenfold greater sensitivity than the G3-treated slide. These results suggest that the E72G3 is useful for simple and effective immobilization of antibodies and can be used to fabricate any immuno devices.
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Affiliation(s)
- Gen Tanaka
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Takahashi F, Funabashi H, Mie M, Endo Y, Sawasaki T, Aizawa M, Kobatake E. Activity-based in vitro selection of T4 DNA ligase. Biochem Biophys Res Commun 2005; 336:987-93. [PMID: 16157309 DOI: 10.1016/j.bbrc.2005.08.200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Accepted: 08/25/2005] [Indexed: 11/25/2022]
Abstract
Recent in vitro methodologies for selection and directed evolution of proteins have concentrated not only on proteins with affinity such as single-chain antibody but also on enzymes. We developed a display technology for selection of T4 DNA ligase on ribosome because an in vitro selection method for DNA ligase had never been developed. The 3' end of mRNA encoding the gene of active or inactive T4 DNA ligase-spacer peptide fusion protein was hybridized to dsDNA fragments with cohesive ends, the substrate of T4 DNA ligase. After in vitro translation of the mRNA-dsDNA complex in a rabbit reticulocyte system, a mRNA-dsDNA-ribosome-ligase complex was produced. T4 DNA ligase enzyme displayed on a ribosome, through addition of a spacer peptide, is able to react with dsDNA in the complex. The complex expressing active ligase was biotinylated by ligation with another biotinylated dsDNA probe and selected with streptavidin-coated magnetic beads. We effectively selected active T4 DNA ligase from a small amount of protein. The gene of the active T4 DNA ligase was enriched 40 times from a mixture of active and inactive genes using this selection strategy. This ribosomal display strategy may have high potential to be useful for selection of other enzymes associated with DNA.
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Affiliation(s)
- Fumio Takahashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Funabashi H, Ishikawa M, Mie M, Takahashi F, Yanagida Y, Aizawa M, Kobatake E. Electrochemical evaluation of cellular physiological status under stress in Escherichia coli with the rpoS-lacZ reporter gene. Biotechnol Bioeng 2005; 90:509-15. [PMID: 15782408 DOI: 10.1002/bit.20459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We developed an electrochemical detection method for evaluating cellular physiological status based on the stringent response as a means to monitor cell viability. A reporter plasmid was constructed by inserting the beta-galactosidase gene (lacZ) under the control of the rpoS promoter, and then used to transform E. coli cells. Electrochemical responses from the products catalyzed by beta-galactosidase expressed by these E. coli cells were detected using the chronoamperometric technique in a nondestructive manner. Comparisons of response currents between the relA-positive strain and relA-negative strain revealed that increases in these currents were caused by the stringent response due to the stressful alcoholic environment, and thus as a model of stressful cultivating conditions. The current was proportional to the beta-galactosidase activity assayed by a conventional method that required the destruction of cells. The cellular physiological status, which depends on the stringent response as a viability marker, therefore, could then be evaluated online with a current using the rpoS-lacZ reporter gene in the relA-positive strain without pretreatment.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
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