1
|
Kudo K, Nishimura T, Izumikawa M, Kozone I, Hashimoto J, Fujie M, Suenaga H, Ikeda H, Satoh N, Shin-Ya K. Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds. J Antibiot (Tokyo) 2024; 77:288-298. [PMID: 38438499 DOI: 10.1038/s41429-024-00711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
Abstract
The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.
Collapse
Affiliation(s)
- Kei Kudo
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Hikaru Suenaga
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
| |
Collapse
|
2
|
Sakata S, Li J, Yasuno Y, Shinada T, Shin-Ya K, Katsuyama Y, Ohnishi Y. Identification of the Cirratiomycin Biosynthesis Gene Cluster in Streptomyces Cirratus: Elucidation of the Biosynthetic Pathways for 2,3-Diaminobutyric Acid and Hydroxymethylserine. Chemistry 2024:e202400271. [PMID: 38456538 DOI: 10.1002/chem.202400271] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Cirratiomycin, a heptapeptide with antibacterial activity, was isolated and characterized in 1981; however, its biosynthetic pathway has not been elucidated. It contains several interesting nonproteinogenic amino acids, such as (2S,3S)-2,3-diaminobutyric acid ((2S,3S)-DABA) and α-(hydroxymethyl)serine, as building blocks. Here, we report the identification of a cirratiomycin biosynthetic gene cluster in Streptomyces cirratus. Bioinformatic analysis revealed that several Streptomyces viridifaciens and Kitasatospora aureofaciens strains also have this cluster. One S. viridifaciens strain was confirmed to produce cirratiomycin. The biosynthetic gene cluster was shown to be responsible for cirratiomycin biosynthesis in S. cirratus in a gene inactivation experiment using CRISPR-cBEST. Interestingly, this cluster encodes a nonribosomal peptide synthetase (NRPS) composed of 12 proteins, including those with an unusual domain organization: a stand-alone adenylation domain, two stand-alone condensation domains, two type II thioesterases, and two NRPS modules that have no adenylation domain. Using heterologous expression and in vitro analysis of recombinant enzymes, we revealed the biosynthetic pathway of (2S,3S)-DABA: (2S,3S)-DABA is synthesized from l-threonine by four enzymes, CirR, CirS, CirQ, and CirB. In addition, CirH, a glycine/serine hydroxymethyltransferase homolog, was shown to synthesize α-(hydroxymethyl)serine from d-serine in vitro. These findings broaden our knowledge of nonproteinogenic amino acid biosynthesis.
Collapse
Affiliation(s)
- Shunki Sakata
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jiafeng Li
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
3
|
Hashimoto T, Suenaga H, Amagai K, Hashimoto J, Kozone I, Takahashi S, Shin-Ya K. In Vitro Module Editing Of NRPS Enables Production Of Highly Potent G q -Signaling Inhibitor FR900359 Derived From Unculturable Plant Symbiont. Angew Chem Int Ed Engl 2024; 63:e202317805. [PMID: 38238265 DOI: 10.1002/anie.202317805] [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: 11/22/2023] [Indexed: 02/03/2024]
Abstract
Heterotrimeric G proteins are key mediators in the signaling of G protein-coupled receptors (GPCR) that are involved in a plethora of important physiological processes and thus major targets of pharmaceutical drugs. The cyclic depsipeptides YM-254890 and FR900359 are strong and selective inhibitors of the Gq subfamily of G proteins. FR900359 was first reported to be produced by unculturable plant symbiont, however, a culturable FR900359 producer was discovered recently by the standard strategy, screening of the producing strain from the environment. As another strategy, we introduce herein the different way to supply natural compounds of unculturable microorganism origin. We therefore embarked on constructing an artificial biosynthetic gene cluster (BGC) for FR900359 with YM-254890 BGC as a template using "in vitro module editing" technology, first developed for the modification of type-I PKS BGCs, to edit YM-254890 BGC. The resulting artificial BGCs coding FR900359 were heterologously expressed in the Pseudomonas putida KT2440 host strain.
Collapse
Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Keita Amagai
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| |
Collapse
|
4
|
Suzuki S, Saito S, Narushima Y, Kodani S, Kagaya N, Suenaga H, Shin-Ya K, Arai MA. Notch activator cyclopiazonic acid induces apoptosis in HL-60 cells through calcineurin activation. J Antibiot (Tokyo) 2024; 77:30-38. [PMID: 37938761 DOI: 10.1038/s41429-023-00673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
We screened a library of microbial extracts and compounds library using our constructed assay cells and found pulicatins F (1) and G (2), and cyclopiazonic acid (CPA) (3) as Notch activators. Pulicatin F (1) and (±)-pulicatin G were synthesized and their activities were evaluated. Notch activation of CPA (3) was investigated using Western blot and RT-PCR. CPA (3) increased protein level of HES1 and mRNA expression of HES1. Also, the expression of FMS-like tyrosine kinase 3 (FLT3), which was known to inhibit apoptosis, was also inhibited by CPA (3) addition. The Notch activation by CPA (3) and cytotoxicity against HL-60 were clearly canceled by addition of FK506, which is an inhibitor of calcineurin (CaN). In addition, it was revealed that CPA (3) induced apoptosis in HL-60 cells.
Collapse
Affiliation(s)
- Shiina Suzuki
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Shun Saito
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Narushima
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Shunta Kodani
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Noritaka Kagaya
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Midori A Arai
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
| |
Collapse
|
5
|
Arima K, Akiyama S, Shin-Ya K, Matsuda K, Wakimoto T. Carrier Protein Mediated Formation of the Dihydropyridazinone Ring in Actinopyridazinone Biosynthesis. Angew Chem Int Ed Engl 2023:e202305155. [PMID: 37194491 DOI: 10.1002/anie.202305155] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/18/2023]
Abstract
Heterocycles with nitrogen-nitrogen (N-N) bonds are privileged building blocks of synthetic drugs. They are also found in natural products, although the biosynthetic logic behind them is poorly understood. Actinopyridazinones produced by Streptomyces sp. MSD090630SC-05 possess unique dihydropyridazinone rings that have been studied as core nuclei in several approved synthetic therapeutics. Herein, we performed gene knockouts and in vitro biochemical experiments to elucidate the major steps in actinopyridazinone biosynthesis, including the unprecedented carrier protein mediated machinery for dihydropyridazinone formation.
Collapse
Affiliation(s)
- Kuga Arima
- Hokkaido University Faculty of Pharmaceutical Sciences: Hokkaido Daigaku Yakugakubu Daigakuin Yakugaku Kenkyuin, Faculty of Pharmaceutical Sciences, JAPAN
| | - Satoko Akiyama
- Hokkaido University Faculty of Pharmaceutical Sciences: Hokkaido Daigaku Yakugakubu Daigakuin Yakugaku Kenkyuin, Faculty of Pharmaceutical Sciences, JAPAN
| | - Kazuo Shin-Ya
- AIST: Kokuritsu Kenkyu Kaihatsu Hojin Sangyo Gijutsu Sogo Kenkyujo, CMB, JAPAN
| | - Kenichi Matsuda
- Hokkaido University Faculty of Pharmaceutical Sciences: Hokkaido Daigaku Yakugakubu Daigakuin Yakugaku Kenkyuin, Faculty of Pharmaceutical Sciences, JAPAN
| | - Toshiyuki Wakimoto
- Hokkaido University, Faculty of Pharmaceutical Sciences, Kita-12, Nishi-6, Kita-ku, 060-0812, Sapporo, JAPAN
| |
Collapse
|
6
|
Kudo F, Kishikawa K, Tsuboi K, Kido T, Usui T, Hashimoto J, Shin-Ya K, Miyanaga A, Eguchi T. Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. Chembiochem 2023; 24:e202200670. [PMID: 36602093 DOI: 10.1002/cbic.202200670] [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: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.
Collapse
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kazuma Tsuboi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takafusa Kido
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| |
Collapse
|
7
|
Kudo F, Minato A, Sato S, Nagano N, Maruyama C, Hamano Y, Hashimoto J, Kozone I, Shin-Ya K, Eguchi T. Mechanism of S-Adenosyl-l-methionine C-Methylation by Cobalamin-dependent Radical S-Adenosyl-l-methionine Methylase in 1-Amino-2-methylcyclopropanecarboxylic Acid Biosynthesis. Org Lett 2022; 24:8975-8979. [PMID: 36458844 DOI: 10.1021/acs.orglett.2c03555] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 12/05/2022]
Abstract
The radical S-adenosyl-l-methionine (SAM) methylase Orf29 catalyzes the C-methylation of SAM in the biosynthesis of 1-amino-2-methylcyclopropanecarboxylic acid. Here, we determined that the methylation product is (4″R)-4″-methyl-SAM. Furthermore, we found that the 5'-deoxyadenosyl radical generated by Orf29 abstracts the pro-R hydrogen atom from the C-4″ position of SAM to generate the radical intermediate, which reacts with methylcobalamin to give (4″R)-4″-methyl-SAM. Consequently, the Orf29-catalyzed C-methylation was confirmed to proceed with retention of configuration.
Collapse
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Atsushi Minato
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Shusuke Sato
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Nayuta Nagano
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Yoshida-Gun, Fukui 910-1195, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Yoshida-Gun, Fukui 910-1195, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| |
Collapse
|
8
|
Matsuda K, Arima K, Akiyama S, Yamada Y, Abe Y, Suenaga H, Hashimoto J, Shin-Ya K, Nishiyama M, Wakimoto T. A Natural Dihydropyridazinone Scaffold Generated from a Unique Substrate for a Hydrazine-Forming Enzyme. J Am Chem Soc 2022; 144:12954-12960. [PMID: 35771530 DOI: 10.1021/jacs.2c05269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nitrogen-nitrogen bond-containing functional groups are rare, but they are found in a considerably wide class of natural products. Recent clarifications of the biosynthetic routes for such functional groups shed light onto overlooked biosynthetic genes distributed across the bacterial kingdom, highlighting the presence of yet-to-be identified natural products with peculiar functional groups. Here, the genome-mining approach targeting a unique hydrazine-forming gene led to the discovery of actinopyridazinones A (1) and B (2), the first natural products with dihydropyridazinone rings. The structure of actinopyridazinone A was unambiguously established by total synthesis. Biosynthetic studies unveiled the structural diversity of natural hydrazines derived from this family of N-N bond-forming enzymes.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoko Akiyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuito Yamada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Yo Abe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Makoto Nishiyama
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| |
Collapse
|
9
|
Sasaki K, Suzuki M, Sonoda T, Schneider-Poetsch T, Ito A, Takagi M, Fujishiro S, Sohtome Y, Dodo K, Umehara T, Aburatani H, Shin-Ya K, Nakao Y, Sodeoka M, Yoshida M. Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells. Cell Chem Biol 2022; 29:1153-1161.e5. [PMID: 35728598 DOI: 10.1016/j.chembiol.2022.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/19/2021] [Revised: 02/05/2022] [Accepted: 05/23/2022] [Indexed: 11/26/2022]
Abstract
Histone lysine methylation is an epigenetic mark that can control gene expression. In particular, H3K9me3 contributes to transcriptional repression by regulating chromatin structure. Successful mitotic progression requires correct timing of chromatin structure changes, including epigenetic marks. However, spatiotemporal information on histone modifications in living cells remains limited. In this study, we created an FRET-based probe for live-cell imaging based on the HP1α chromodomain (HP1αCD), which binds to H3K9me3. The probe was incorporated into chromatin and the emission ratio decreased after treatment with histone methyltransferase inhibitors, indicating that it successfully traced dynamic changes in H3K9me3. Upon entry into mitosis, the probe's emission ratio transiently increased with a concomitant increase in H3K9me3, then exhibited a stepwise decrease, probably due to loss of HP1αCD binding caused by phosphorylation of H3S10 and demethylation of H3K9me3. This probe will be a useful tool for detecting dynamic changes in chromatin structure associated with HP1α.
Collapse
Affiliation(s)
- Kazuki Sasaki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.
| | - Michihiro Suzuki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Sonoda
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, 135-0064, Japan
| | - Shinya Fujishiro
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Aburatani
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan; Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoichi Nakao
- Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan; Research Institute for Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| |
Collapse
|
10
|
Rider SD, Gadgil RY, Hitch DC, Damewood FJ, Zavada N, Shanahan M, Alhawach V, Shrestha R, Shin-Ya K, Leffak M. Stable G-quadruplex DNA structures promote replication-dependent genome instability. J Biol Chem 2022; 298:101947. [PMID: 35447109 PMCID: PMC9142560 DOI: 10.1016/j.jbc.2022.101947] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 10/27/2022] Open
Abstract
G-quadruplex (G4)-prone structures are abundant in mammalian genomes, where they have been shown to influence DNA replication, transcription, and genome stability. In this article, we constructed cells with a single ectopic homopurine/homopyrimidine repeat tract derived from the polycystic kidney disease type 1 (PKD1) locus, which is capable of forming triplex (H3) and G4 DNA structures. We show that ligand stabilization of these G4 structures results in deletions of the G4 consensus sequence, as well as kilobase deletions spanning the G4 and ectopic sites. Furthermore, we show that DNA double-strand breaks at the ectopic site are dependent on the nuclease Mus81. Hypermutagenesis during sister chromatid repair extends several kilobases from the G4 site and breaks at the G4 site resulting in microhomology-mediated translocations. To determine whether H3 or G4 structures are responsible for homopurine/homopyrimidine tract instability, we derived constructs and cell lines from the PKD1 repeat, which can only form H3 or G4 structures. Under normal growth conditions, we found that G4 cell lines lost the G4 consensus sequence early during clonal outgrowth, whereas H3 cells showed DNA instability early during outgrowth but only lost reporter gene expression after prolonged growth. Thus, both the H3 and G4 non-B conformation DNAs exhibit genomic instability, but they respond differently to endogenous replication stress. Our results show that the outcomes of replication-dependent double-strand breaks at non-B-DNAs model the instability observed in microhomology-mediated break-induced replication (BIR). Marked variability in the frequency of mutagenesis during BIR suggests possible dynamic heterogeneity in the BIR replisome.
Collapse
Affiliation(s)
- S Dean Rider
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - David C Hitch
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Nathen Zavada
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Matilyn Shanahan
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Venicia Alhawach
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Resha Shrestha
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA.
| |
Collapse
|
11
|
Tsutsumi H, Moriwaki Y, Terada T, Shimizu K, Shin-Ya K, Katsuyama Y, Ohnishi Y. Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase. Angew Chem Int Ed Engl 2021; 61:e202111217. [PMID: 34626048 DOI: 10.1002/anie.202111217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/19/2021] [Indexed: 11/11/2022]
Abstract
Prenyl pyrophosphate methyltransferases enhance the structural diversity of terpenoids. However, the molecular basis of their catalytic mechanisms is poorly understood. In this study, using multiple strategies, we characterized a geranyl pyrophosphate (GPP) C6-methyltransferase, BezA. Biochemical analysis revealed that BezA requires Mg2+ and solely methylates GPP. The crystal structures of BezA and its complex with S-adenosyl homocysteine were solved at 2.10 and 2.56 Å, respectively. Further analyses using site-directed mutagenesis, molecular docking, molecular dynamics simulations, and quantum mechanics/molecular mechanics calculations revealed the molecular basis of the methylation reaction. Importantly, the function of E170 as a catalytic base to complete the methylation reaction was established. We also succeeded in switching the substrate specificity by introducing a W210A substitution, resulting in an unprecedented farnesyl pyrophosphate C6-methyltransferase.
Collapse
Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Technology Research Association for Next Generation Natural Products Chemistry, 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
12
|
Seimiya H, Nagasawa K, Shin-Ya K. Chemical targeting of G-quadruplexes in telomeres and beyond for molecular cancer therapeutics. J Antibiot (Tokyo) 2021; 74:617-628. [PMID: 34285374 DOI: 10.1038/s41429-021-00454-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
G-quadruplexes (G4s) are higher-order structures formed by guanine-rich sequences of nucleic acids, such as the telomeric 5'-TTAGGG-3'/5'-UUAGGG-3' repeats and those in gene regulatory regions. G4s regulate various biological events, including replication, transcription, and translation. Imbalanced G4 dynamics is associated with diseases, such as cancer and neurodegenerative diseases. Telomestatin is a natural macrocyclic compound derived from Streptomyces anulatus 3533-SV4. It interacts with the guanine quartet via π-π stacking and potently stabilizes G4. Because G4 stabilization at the telomeric repeat inhibits the telomere-synthesizing enzyme telomerase, telomestatin was originally identified as a telomerase inhibitor. Whereas non-toxic doses of telomestatin induce gradual shortening of telomeres and eventual crisis in human cancer cells, higher doses trigger prompt replication stress and DNA damage responses, resulting in acute cell death. Suppression of the transcription and translation of G4-containing genes is also implicated in the anticancer effects of telomestatin. Because telomestatin is rare, labile, and insoluble, synthetic oxazole telomestatin derivatives have been developed and verified for their therapeutic efficacies in preclinical cancer models. Furthermore, a variety of G4-stabilizing compounds have been reported as promising seeds for molecular cancer therapeutics. To improve the design of future clinical studies, it will be important to identify predictive biomarkers of drug efficacy.
Collapse
Affiliation(s)
- Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Technology Research Association for Next Generation Natural Products Chemistry, Tokyo, Japan
| |
Collapse
|
13
|
Katsuyama Y, Sone K, Harada A, Kawai S, Urano N, Adachi N, Moriya T, Kawasaki M, Shin-Ya K, Senda T, Ohnishi Y. Structural and Functional Analyses of the Tridomain-Nonribosomal Peptide Synthetase FmoA3 for 4-Methyloxazoline Ring Formation. Angew Chem Int Ed Engl 2021; 60:14554-14562. [PMID: 33783097 DOI: 10.1002/anie.202102760] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 02/23/2021] [Indexed: 11/08/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are attractive targets for bioengineering to generate useful peptides. FmoA3 is a single modular NRPS composed of heterocyclization (Cy), adenylation (A), and peptidyl carrier protein (PCP) domains. It uses α-methyl-l-serine to synthesize a 4-methyloxazoline ring, probably with another Cy domain in the preceding module FmoA2. Here, we determined the head-to-tail homodimeric structures of FmoA3 by X-ray crystallography (apo-form, with adenylyl-imidodiphosphate and α-methyl-l-seryl-AMP) and cryogenic electron microscopy single particle analysis, and performed site-directed mutagenesis experiments. The data revealed that α-methyl-l-serine can be accommodated in the active site because of the extra space around Ala688. The Cy domains of FmoA2 and FmoA3 catalyze peptide bond formation and heterocyclization, respectively. FmoA3's Cy domain seems to lose its donor PCP binding activity. The collective data support a proposed catalytic cycle of FmoA3.
Collapse
Affiliation(s)
- Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kaoru Sone
- Department of Biotechnology, Graduate School of Agricultural and Life science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ayaka Harada
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Seiji Kawai
- Department of Biotechnology, Graduate School of Agricultural and Life science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naoki Urano
- Department of Biotechnology, Graduate School of Agricultural and Life science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
14
|
Nishimura T, Kawahara T, Kagaya N, Ogura Y, Takikawa H, Suenaga H, Adachi M, Hirokawa T, Doi T, Shin-Ya K. JBIR-155, a Specific Class D β-Lactamase Inhibitor of Microbial Origin. Org Lett 2021; 23:4415-4419. [PMID: 34029112 DOI: 10.1021/acs.orglett.1c01352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We discovered JBIR-155 as a novel specific class D β-lactamase inhibitor from Streptomyces polymachus SoB100815Hv02. JBIR-155 consists of a 6-oxabicyclo[3.2.0]heptan-7-one skeleton and a long unsaturated alkyl chain moiety of which absolute configuration was determined by spectroscopic data, modified Mosher's method, and analyses of the relative configuration of chemically modified derivative. JBIR-155 specifically exhibited inhibitory activity against the class D β-lactamase, with an IC50 value of 0.36 μM.
Collapse
Affiliation(s)
- Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064 Japan
| | - Noritaka Kagaya
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yusuke Ogura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masaatsu Adachi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takatsugu Hirokawa
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kazuo Shin-Ya
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
15
|
Kudo K, Nishimura T, Kozone I, Hashimoto J, Kagaya N, Suenaga H, Ikeda H, Shin-Ya K. Hemiacetal-less rapamycin derivatives designed and produced by genetic engineering of a type I polyketide synthase. Sci Rep 2021; 11:9944. [PMID: 33976244 PMCID: PMC8113240 DOI: 10.1038/s41598-021-88583-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/14/2021] [Indexed: 11/09/2022] Open
Abstract
Engineering polyketide synthases is one of the most promising ways of producing a variety of polyketide derivatives. Exploring the undiscovered chemical space of this medicinally important class of middle molecular weight natural products will aid in the development of improved drugs in the future. In previous work, we established methodology designated 'module editing' to precisely manipulate polyketide synthase genes cloned in a bacterial artificial chromosome. Here, in the course of investigating the engineering capacity of the rapamycin PKS, novel rapamycin derivatives 1-4, which lack the hemiacetal moiety, were produced through the heterologous expression of engineered variants of the rapamycin PKS. Three kinds of module deletions in the polyketide synthase RapC were designed, and the genetically engineered vectors were prepared by the in vitro module editing technique. Streptomyces avermitilis SUKA34 transformed with these edited PKSs produced new rapamycin derivatives. The planar structures of 1-4 established based on 1D and 2D NMR, ESI-TOF-MS and UV spectra revealed that 2 and 3 had skeletons well-matched to the designs, but 1 and 4 did not. The observations provide important insights into the mechanisms of the later steps of rapamycin skeletal formation as well as the ketone-forming oxygenase RapJ.
Collapse
Affiliation(s)
- Kei Kudo
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, Japan
| | - Noritaka Kagaya
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, Japan. .,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
16
|
Liu C, Hashimoto J, Kudo K, Shin-Ya K, Kakeya H. An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides. Chem Asian J 2021; 16:1382-1387. [PMID: 33886165 DOI: 10.1002/asia.202100181] [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: 02/21/2021] [Revised: 04/02/2021] [Indexed: 11/07/2022]
Abstract
The incorporation of non-proteinogenic amino acids (NPAAs) enriches the structural diversity of nonribosomal peptides. Recently, four NPAA-containing cyclic hexapeptides, longicatenamides A-D, were isolated using a combined-culture strategy. Based on in silico analysis, we discovered their putative biosynthetic gene cluster (lon) and proposed a possible biosynthetic mechanism. Surprisingly, the lon22 gene encodes an atypical arginine dihydrolase, which can also catalyze the hydrolysis of citrulline to ornithine. Phylogenetic analysis showed that Lon22-like proteins form a novel clade that is separated from other guanidine-modifying enzymes. After rational design, the catalytic efficiencies of a Lon22 Y80F mutant for arginine and citrulline substrates were 2.31- and 4.70-fold that of the wild-type (WT), respectively. In addition, characterization of the Lon20-A4 adenylation domain suggested that it can incorporate both ornithine and lysine into the final products.
Collapse
Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| |
Collapse
|
17
|
Ueoka R, Hashimoto J, Kozone I, Hashimoto T, Kudo K, Kagaya N, Suenaga H, Ikeda H, Shin-Ya K. A novel methymycin analog, 12-ketomethymycin N-oxide, produced by the heterologous expression of the large pikromycin/methymycin biosynthetic gene cluster of Streptomyces sp. AM4900. Biosci Biotechnol Biochem 2021; 85:890-894. [PMID: 33590846 DOI: 10.1093/bbb/zbaa111] [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: 11/05/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022]
Abstract
A novel methymycin analog, 12-ketomethymycin N-oxide, was produced by the heterologous expression of the pikromycin/methymycin biosynthetic gene cluster of Streptomyces sp. AM4900 together with 12-ketomethymycin, which was only isolated by the biotransformation of the synthetic intermediate before. Their structures were determined by the spectroscopic data and the chemical derivatization. 12-Ketomethymycin showed a weak cytotoxicity against SKOV-3 and Jurkat cells, although its N-oxide analog did not show any activity. Both showed no antibacterial activities against Escherichia coli and Micrococcus luteus.
Collapse
Affiliation(s)
- Reiko Ueoka
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Kanagawa, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
18
|
Hashimoto T, Hashimoto J, Kagaya N, Nishimura T, Suenaga H, Nishiyama M, Kuzuyama T, Shin-Ya K. A novel oxazole-containing tetraene compound, JBIR-159, produced by heterologous expression of the cryptic trans-AT type polyketide synthase biosynthetic gene cluster. J Antibiot (Tokyo) 2021; 74:354-358. [PMID: 33558648 DOI: 10.1038/s41429-021-00410-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 11/09/2022]
Abstract
Using genome mining approach, we identified a novel biosynthetic gene cluster containing trans-AT type PKS genes from Streptomyces versipellis 4083-SVS6. A bacterial artificial chromosome (BAC) clone, pKU503JL68_PN1_P10-C12, accommodating the entire biosynthetic gene cluster was obtained from a BAC library. Heterologous expression of the biosynthetic gene cluster in Streptomyces lividans TK23 led to the production of a novel polyene compound, JBIR-159. We report herein the biosynthetic gene cluster for JBIR-159, and the heterologous expression, isolation, structure determination and a brief biological activity.
Collapse
Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, Tokyo, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tomohisa Kuzuyama
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. .,Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
19
|
Khaledian B, Taguchi A, Shin-Ya K, Kondo-Ida L, Kagaya N, Suzuki M, Kajino T, Yamaguchi T, Shimada Y, Takahashi T. Inhibition of heat shock protein 90 destabilizes receptor tyrosine kinase ROR1 in lung adenocarcinoma. Cancer Sci 2021; 112:1225-1234. [PMID: 33370472 PMCID: PMC7935804 DOI: 10.1111/cas.14786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/20/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023] Open
Abstract
We have previously identified receptor tyrosine kinase‐like orphan receptor 1 (ROR1) as a direct transcriptional target of TTF‐1/NKX2‐1, a lineage‐survival oncogene in lung adenocarcinoma. ROR1 sustains prosurvival signaling from multiple receptor tyrosine kinases including epidermal growth factor receptor, MET, and insulin‐like growth factor 1 receptor in part by maintaining the caveolae structure as a scaffold protein of cavin‐1 and caveolin‐1. In this study, a high throughput screening of the natural product library containing 2560 compounds was undertaken using a cell‐based FluoPPI assay detecting ROR1‐cavin‐1 interaction. As a result, geldanamycin (GA), a known inhibitor of heat shock protein 90 (HSP90), was identified as a potential inhibitor of ROR1. Geldanamycin, as well as two GA derivatives tested in the clinic, 17‐allylamino‐17‐demethoxygeldanamycin (17‐AAG) and 17‐dimethylaminoethylamino‐17‐demethoxygeldanamycin (17‐DMAG), decreased ROR1 protein expression. We found that ROR1 physically interacted with HSP90α, but not with other HSP90 paralogs, HSP90β or GRP94. Geldanamycin in turn destabilized and degraded ROR1 protein in a dose‐ and time‐dependent manner through the ubiquitin/proteasome pathway, resulting in a significant suppression of cell proliferation in lung adenocarcinoma cell lines, for which the kinase domain of ROR1, but not its kinase activity or N‐glycosylation, was required. Our findings indicate that HSP90 is required to sustain expression of ROR1 crucial for lung adenosarcoma survival, suggesting that inhibition of HSP90 could be a promising therapeutic strategy in ROR1‐positive lung adenocarcinoma.
Collapse
Affiliation(s)
- Behnoush Khaledian
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Lisa Kondo-Ida
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Motoshi Suzuki
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Oncology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Taisuke Kajino
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoya Yamaguchi
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
| | - Yukako Shimada
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Takahashi
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Aichi Cancer Center, Nagoya, Japan
| |
Collapse
|
20
|
Nogawa T, Terai A, Amagai K, Hashimoto J, Futamura Y, Okano A, Fujie M, Satoh N, Ikeda H, Shin-Ya K, Osada H, Takahashi S. Heterologous Expression of the Biosynthetic Gene Cluster for Verticilactam and Identification of Analogues. J Nat Prod 2020; 83:3598-3605. [PMID: 33216528 DOI: 10.1021/acs.jnatprod.0c00755] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Verticilactam and the new geometric isomers, verticilactams B and C, were produced by heterologous expression of the biosynthetic gene cluster for verticilactam using the Streptomyces avermitilis SUKA17 strain. Only verticilactam, a compound with a characteristic β-ketoamide unit within a 16-membered polyketide macrolactam conjugated with an octalin skeleton, had been previously reported having been isolated from Streptomyces spiroverticillatus JC-8444. In this report, minor verticilactam derivatives were isolated from the transformed strain, and their structures elucidated by spectral analysis. Verticilactam B was a geometric isomer at Δ17 and Δ19, and verticilactam C was the Δ19 and Δ21 isomer. In addition, the absolute configuration of verticilactam was confirmed by ECD analysis and NMR chemical shifts. The stereochemistry assignments of the hydroxy groups at C-10 and C-12 were supported by the domain organization of the polyketide synthase identified in the verticilactam gene cluster. Verticilactam showed moderate activity against the malaria parasite Plasmodium falciparum 3D7 strain with no significant cytotoxicity or antimicrobial effects.
Collapse
Affiliation(s)
- Toshihiko Nogawa
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsutaka Terai
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Keita Amagai
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yushi Futamura
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akiko Okano
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1, Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
21
|
Ueoka R, Shinzato N, Kagaya N, Suenaga H, Shin-Ya K. Pseudoalteropeptide A, a novel lipopeptide from the marine bacterium Pseudoalteromonas piscicida SWA4_PA4 isolated from marine seaweed. J Antibiot (Tokyo) 2020; 74:105-110. [PMID: 33060815 DOI: 10.1038/s41429-020-00377-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/29/2023]
Abstract
A new lipopeptide, pseudoalteropeptide A (1) was isolated from the marine bacterium Pseudoalteromonas piscicida SWA4_PA4. The structure was elucidated by spectroscopic analyses including NMR and MSMS spectra. It showed moderate iron chelating activity as well as cytotoxic activity against Jurkat human T lymphocyte cells. isolation/marine bacterium/natural product/structure elucidation.
Collapse
Affiliation(s)
- Reiko Ueoka
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Naoya Shinzato
- Center of Molecular Biosciences, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 902-0213, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. .,Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
22
|
Bastola S, Pavlyukov MS, Yamashita D, Ghosh S, Cho H, Kagaya N, Zhang Z, Minata M, Lee Y, Sadahiro H, Yamaguchi S, Komarova S, Yang E, Markert J, Nabors LB, Bhat K, Lee J, Chen Q, Crossman DK, Shin-Ya K, Nam DH, Nakano I. Glioma-initiating cells at tumor edge gain signals from tumor core cells to promote their malignancy. Nat Commun 2020; 11:4660. [PMID: 32938908 PMCID: PMC7494913 DOI: 10.1038/s41467-020-18189-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 04/23/2019] [Accepted: 07/23/2020] [Indexed: 01/07/2023] Open
Abstract
Intratumor spatial heterogeneity facilitates therapeutic resistance in glioblastoma (GBM). Nonetheless, understanding of GBM heterogeneity is largely limited to the surgically resectable tumor core lesion while the seeds for recurrence reside in the unresectable tumor edge. In this study, stratification of GBM to core and edge demonstrates clinically relevant surgical sequelae. We establish regionally derived models of GBM edge and core that retain their spatial identity in a cell autonomous manner. Upon xenotransplantation, edge-derived cells show a higher capacity for infiltrative growth, while core cells demonstrate core lesions with greater therapy resistance. Investigation of intercellular signaling between these two tumor populations uncovers the paracrine crosstalk from tumor core that promotes malignancy and therapy resistance of edge cells. These phenotypic alterations are initiated by HDAC1 in GBM core cells which subsequently affect edge cells by secreting the soluble form of CD109 protein. Our data reveal the role of intracellular communication between regionally different populations of GBM cells in tumor recurrence. Intratumoural spatial heterogeneity is crucial to enhance therapeutic resistance in glioblastoma. Here, the authors show a paracrine signaling mechanism where glioblastoma-initiating cells located in the tumour edge elevate their malignancy by interaction with core-located tumour cells.
Collapse
Affiliation(s)
- Soniya Bastola
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russian Federation
| | - Daisuke Yamashita
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Sadashib Ghosh
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Heejin Cho
- Research Institute for Future Medicine, Seoul, 06351, Republic of Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Noritaka Kagaya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Zhuo Zhang
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Mutsuko Minata
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yeri Lee
- Research Institute for Future Medicine, Seoul, 06351, Republic of Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | | | - Shinobu Yamaguchi
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Svetlana Komarova
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Eddy Yang
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - James Markert
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Louis B Nabors
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Krishna Bhat
- Department of Translational Molecular Pathology and Brain Tumor Center, The University of Texas, M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - James Lee
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Qin Chen
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Integrative medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.,Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Research and Development Center for Precision Medicine, Tsukuba University, Tsukuba, Japan.
| |
Collapse
|
23
|
Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
Collapse
Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
| |
Collapse
|
24
|
Kataura T, Tashiro E, Nishikawa S, Shibahara K, Muraoka Y, Miura M, Sakai S, Katoh N, Totsuka M, Onodera M, Shin-Ya K, Miyamoto K, Sasazawa Y, Hattori N, Saiki S, Imoto M. A chemical genomics-aggrephagy integrated method studying functional analysis of autophagy inducers. Autophagy 2020; 17:1856-1872. [PMID: 32762399 PMCID: PMC8386610 DOI: 10.1080/15548627.2020.1794590] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Macroautophagy/autophagy plays a critical role in the pathogenesis of various human diseases including neurodegenerative disorders such as Parkinson disease (PD) and Huntington disease (HD). Chemical autophagy inducers are expected to serve as disease-modifying agents by eliminating cytotoxic/damaged proteins. Although many autophagy inducers have been identified, their precise molecular mechanisms are not fully understood because of the complicated crosstalk among signaling pathways. To address this issue, we performed several chemical genomic analyses enabling us to comprehend the dominancy among the autophagy-associated pathways followed by an aggresome-clearance assay. In a first step, more than 400 target-established small molecules were assessed for their ability to activate autophagic flux in neuronal PC12D cells, and we identified 39 compounds as autophagy inducers. We then profiled the autophagy inducers by testing their effect on the induction of autophagy by 200 well-established signal transduction modulators. Our principal component analysis (PCA) and clustering analysis using a dataset of "autophagy profiles" revealed that two Food and Drug Administration (FDA)-approved drugs, memantine and clemastine, activate endoplasmic reticulum (ER) stress responses, which could lead to autophagy induction. We also confirmed that SMK-17, a recently identified autophagy inducer, induced autophagy via the PRKC/PKC-TFEB pathway, as had been predicted from PCA. Finally, we showed that almost all of the autophagy inducers tested in this present work significantly enhanced the clearance of the protein aggregates observed in cellular models of PD and HD. These results, with the combined approach, suggested that autophagy-activating small molecules may improve proteinopathies by eliminating nonfunctional protein aggregates.Abbreviations: ADK: adenosine kinase; AMPK: AMP-activated protein kinase; ATF4: activating transcription factor 4; BECN1: beclin-1; DDIT3/CHOP: DNA damage inducible transcript 3; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; EIF2S1/eIF2α: eukaryotic translation initiation factor 2 subunit alpha; ER: endoplasmic reticulum; ERN1/IRE1α: endoplasmic reticulum to nucleus signaling 1; FDA: Food and Drug Administration; GSH: glutathione; HD: Huntington disease; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; HTT: huntingtin; JAK: Janus kinase, MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MAP2K/MEK: mitogen-activated protein kinase kinase; MAP3K8/Tpl2: mitogen-activated protein kinase kinase kinase 8; MAPK: mitogen-activated protein kinase; MPP+: 1-methyl-4-phenylpyridinium; MTOR: mechanistic target of rapamycin kinase; MTORC: MTOR complex; NAC: N-acetylcysteine; NGF: nerve growth factor 2; NMDA: N-methyl-D-aspartate; PCA: principal component analysis; PD: Parkinson disease; PDA: pancreatic ductal adenocarcinoma; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PMA: phorbol 12-myristate 13-acetate; PRKC/PKC: protein kinase C; ROCK: Rho-associated coiled-coil protein kinase; RR: ribonucleotide reductase; SIGMAR1: sigma non-opioid intracellular receptor 1; SQSTM1/p62: sequestosome 1; STK11/LKB1: serine/threonine kinase 11; TFEB: Transcription factor EB; TGFB/TGF-β: Transforming growth factor beta; ULK1: unc-51 like autophagy activating kinase 1; XBP1: X-box binding protein 1.
Collapse
Affiliation(s)
- Tetsushi Kataura
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan.,Research Fellow of the Japan Society for the Promotion of Science (JSPS), Tokyo, Japan
| | - Etsu Tashiro
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Shota Nishikawa
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Kensuke Shibahara
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Yoshihito Muraoka
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Masahiro Miura
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Shun Sakai
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Naohiro Katoh
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Misato Totsuka
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Masafumi Onodera
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Biotechnology Research Centre, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kengo Miyamoto
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Yukiko Sasazawa
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan.,Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Shinji Saiki
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Masaya Imoto
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| |
Collapse
|
25
|
Kurosawa S, Matsuda K, Hasebe F, Shiraishi T, Shin-Ya K, Kuzuyama T, Nishiyama M. Guanidyl modification of the 1-azabicyclo[3.1.0]hexane ring in ficellomycin essential for its biological activity. Org Biomol Chem 2020; 18:5137-5144. [PMID: 32582897 DOI: 10.1039/d0ob00339e] [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: 11/21/2022]
Abstract
The 1-azabicyclo[3.1.0]hexane ring is a key moiety in natural products for biological activities against bacteria, fungi, and tumor through DNA alkylation. Ficellomycin is a dipeptide that consists of l-valine and a non-proteinogenic amino acid with the 1-azabicyclo[3.1.0]hexane ring structure. Although the biosynthetic gene cluster of ficellomycin has been identified, the biosynthetic pathway currently remains unclear. We herein report the final stage of ficellomycin biosynthesis involving ring modifications and successive dipeptide formation. After the ring is formed, the hydroxy group of the ring is converted into the guanidyl unit by three enzymes, which include an aminotransferase with a novel inter ω-ω amino-transferring activity. In the last step, the resulting 1-azabicyclo[3.1.0]hexane ring-containing amino acid is connected with l-valine by an amino acid ligase to yield ficellomycin. The present study revealed a new machinery that expands the structural and biological diversities of natural products.
Collapse
Affiliation(s)
- Sumire Kurosawa
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan.
| | - Kenichi Matsuda
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan.
| | - Fumihito Hasebe
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan.
| | - Taro Shiraishi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan. and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan. and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan. and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8567, Japan
| |
Collapse
|
26
|
Hayakawa Y, Yaguchi R, Akimoto M, Kimata S, Shin-Ya K. Neocurromycin A, a new GRP78 downregulator from Streptomyces sp. RAI364. J Antibiot (Tokyo) 2020; 73:790-793. [PMID: 32572166 DOI: 10.1038/s41429-020-0339-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 01/28/2023]
Abstract
A new curromycin-related compound, neocurromycin A (2), was isolated from the fermented broth of Streptomyces sp. RAI364. The molecular formula of 2 was established as C35H44N4O7 by ESI-MS and the structure was elucidated by NMR spectroscopic analyses. Neocurromycin A showed selective cytotoxicity against MKN45 human gastric cancer cells in a nutrient-deprived medium with an IC50 of 380 nM and inhibited the expression of the molecular chaperone GRP78 in HT1080 G-L cells in the presence of 10 mM of 2-deoxyglucose with an IC50 of 1.7 µM.
Collapse
Affiliation(s)
- Yoichi Hayakawa
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| | - Ryodai Yaguchi
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Minami Akimoto
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shoko Kimata
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| |
Collapse
|
27
|
Hashimoto T, Kozone I, Hashimoto J, Suenaga H, Fujie M, Satoh N, Ikeda H, Shin-Ya K. Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin. J Antibiot (Tokyo) 2020; 73:650-654. [PMID: 32457441 DOI: 10.1038/s41429-020-0319-0] [Citation(s) in RCA: 7] [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] [Received: 03/14/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 01/23/2023]
Abstract
From our in-house microbial genome database of secondary metabolite producers, we identified a candidate biosynthetic gene cluster for desertomycin from Streptomyces nobilis JCM4274. We report herein the cloning of the 127-kb entire gene cluster for desertomycin biosynthesis using bacterial artificial chromosome vector. The entire biosynthetic gene cluster for desertomycin was introduced in the heterologous host, Streptomyces lividans TK23, with an average yield of more than 130 mg l-1.
Collapse
Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. .,The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
28
|
Kawahara T, Itoh M, Izumikawa M, Kagaya N, Sakata N, Tsuchida T, Shin-Ya K. New phenylspirodrimane metabolites MBJ-0030, MBJ-0031, and MBJ-0032 isolated from the soil fungal strain Stachybotrys sp. f23793. Biosci Biotechnol Biochem 2020; 84:1570-1575. [PMID: 32338185 DOI: 10.1080/09168451.2020.1757402] [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] [Indexed: 10/24/2022]
Abstract
Chemical screening of culture medium from the soil fungus Stachybotrys sp. resulted in the isolation of the three new phenylspirodrimanes MBJ-0030 (1), MBJ-0031 (2) and MBJ-0032 (3). Their structures were determined by detailed analysis of spectroscopic data. The absolute configurations of 1-3 were determined by modified Mosher's and Marfey's methods. In addition, cytotoxic and antimicrobial evaluations of the compounds were conducted.
Collapse
Affiliation(s)
- Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC) , Tokyo, Japan
| | - Masashi Itoh
- Research & Development Division, MicroBiopharm Japan Co., Ltd (MBJ) , Iwata, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC) , Tokyo, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo, Japan
| | - Noriaki Sakata
- Research & Development Division, MicroBiopharm Japan Co., Ltd (MBJ) , Iwata, Japan
| | - Toshio Tsuchida
- Research & Development Division, MicroBiopharm Japan Co., Ltd (MBJ) , Iwata, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo, Japan.,The Biotechnology Research Center, The University of Tokyo , Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo , Tokyo, Japan
| |
Collapse
|
29
|
Demachi A, Uchida R, Arima S, Nagamitsu T, Hashimoto J, Komatsu M, Kozone I, Shin-Ya K, Tomoda H, Ikeda H. An Unusual Extender Unit Is Incorporated into the Modular Polyketide Synthase of Scopranones Biosynthesis. Biochemistry 2019; 58:5066-5073. [PMID: 31756295 DOI: 10.1021/acs.biochem.9b00908] [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: 11/28/2022]
Abstract
Scopranones, produced by Streptomyces sp. BYK-11038, are the novel bone morphogenetic protein inhibitors characterized by atypical two scoop-like moieties and a 3-furanone moiety. Two scoop-like moieties connected to a 3-furanone have not previously been reported in natural products, and their biosynthesis must occur via a unique pathway. Feeding experiments using 13C-labeled precursors indicated that scopranones were synthesized from three acetates and three butyrates in polyketide-type biosynthesis. Genome mining of Streptomyces sp. BYK-11038 revealed that the candidate biosynthetic gene cluster contains 21 open reading frames (ORFs), including three modular polyketide synthases (PKSs; SprA, SprB, and SprC), which were composed of 4 modules with one loading module and 18 additional ORFs (SprD to SprU) spanning a distance of 55 kbp. The characterization of in-frame deletion mutants and feeding experiments with the predicted extender units indicated that two genes, sprP and sprR, encoding discrete 3-oxoacyl-ACP synthases, and a gene, sprO, encoding crotonyl-CoA reductase, were involved in assembling an unusual C8 branched extender unit, 2-(2-ethylbutyl)malonyl-CoA. Additionally, three ORFs, sprM, sprN, and sprT, encoding cytochrome P450s and a monooxygenase, are important tailoring enzymes in post-PKS modification. SprT is an essential enzyme for decarboxylative ring contraction via oxidation, which converts the 2-pyranone to a 3-furanone.
Collapse
Affiliation(s)
- Ayumu Demachi
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Ryuji Uchida
- Faculty of Pharmaceutical Sciences , Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku , Sendai , Miyagi 981-8558 , Japan
| | - Shiho Arima
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Tohru Nagamitsu
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium , 2-4-7 Aomi, Koto-ku , Tokyo 135-8073 , Japan
| | - Mamoru Komatsu
- Kitasato Institute for Life Sciences , Kitasato University , 1-15-1 Kitasato, Minami-ku , Sagamihara , Kanagawa 252-0373 , Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium , 2-4-7 Aomi, Koto-ku , Tokyo 135-8073 , Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology , 2-4-7 Aomi, Koto-ku , Tokyo 135-0064 , Japan
| | - Hiroshi Tomoda
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences , Kitasato University , 1-15-1 Kitasato, Minami-ku , Sagamihara , Kanagawa 252-0373 , Japan
| |
Collapse
|
30
|
Murashima A, Shinjo K, Katsushima K, Onuki T, Kondoh Y, Osada H, Kagaya N, Shin-Ya K, Kimura H, Yoshida M, Murakami S, Kondo Y. Identification of a chemical modulator of EZH2-mediated silencing by cell-based high-throughput screening assay. J Biochem 2019; 166:41-50. [PMID: 30690451 DOI: 10.1093/jb/mvz007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Dysregulation of enhancer of zeste homologue 2 (EZH2), a methyltransferase component of polycomb repressive complex 2, is found in many types of cancers especially those that are highly progressive and aggressive. Specific catalytic inhibitors of EZH2 have high anti-tumour activity, particularly in lymphomas with EZH2 activating mutations. However, the clinical benefits of EZH2 catalytic inhibitors in tumours overexpressing EZH2 are still limited. Here, we identified NPD13668, a novel modulator of EZH2-mediated gene silencing, from 329,049 small chemical compounds using a cell-based high-throughput screening assay. NPD13668 reactivated the expression of silenced H3K27me3 target genes together with depletion of the H3K27me3 modification. In addition, NPD13668 repressed the cell growth of prostate cancer cell lines (PC3 and LNCaP) and ovarian cancer cell lines (SKOV3 and NIH-OVCAR3). NPD13668 partially inhibited the methyltransferase activity of EZH2 in vitro. Genome-wide expression analysis revealed that after NPD13668 treatment, about half of the upregulated genes overlapped with genes upregulated after treatment with GSK126, well-known EZH2 catalytic inhibitor, indicating that NPD13668 is a potential modulator of EZH2 methyltransferase activity. Our data demonstrated that targeting the pharmacological inhibition of EZH2 activity by NPD13668 might be a novel cancer treatment.
Collapse
Affiliation(s)
- Akihiro Murashima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan.,Department of Oto-rhino-laryngology and Head-and-neck-surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Tetsuo Onuki
- Chemical Genomics Research Group & Seed Compound Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group & Chemical Resource Development Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group & Chemical Resource Development Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Japan
| | - Noritaka Kagaya
- Department of Life Science and Biotechnology, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Unit. Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Yokohama, Tokyo, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group & Seed Compound Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Japan
| | - Shingo Murakami
- Department of Oto-rhino-laryngology and Head-and-neck-surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| |
Collapse
|
31
|
Bharti SK, Sommers JA, Awate S, Bellani MA, Khan I, Bradley L, King GA, Seol Y, Vidhyasagar V, Wu Y, Abe T, Kobayashi K, Shin-Ya K, Kitao H, Wold MS, Branzei D, Neuman KC, Brosh RM. A minimal threshold of FANCJ helicase activity is required for its response to replication stress or double-strand break repair. Nucleic Acids Res 2019; 46:6238-6256. [PMID: 29788478 PMCID: PMC6159516 DOI: 10.1093/nar/gky403] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 07/21/2017] [Accepted: 05/01/2018] [Indexed: 01/24/2023] Open
Abstract
Fanconi Anemia (FA) is characterized by bone marrow failure, congenital abnormalities, and cancer. Of over 20 FA-linked genes, FANCJ uniquely encodes a DNA helicase and mutations are also associated with breast and ovarian cancer. fancj−/− cells are sensitive to DNA interstrand cross-linking (ICL) and replication fork stalling drugs. We delineated the molecular defects of two FA patient-derived FANCJ helicase domain mutations. FANCJ-R707C was compromised in dimerization and helicase processivity, whereas DNA unwinding by FANCJ-H396D was barely detectable. DNA binding and ATP hydrolysis was defective for both FANCJ-R707C and FANCJ-H396D, the latter showing greater reduction. Expression of FANCJ-R707C or FANCJ-H396D in fancj−/− cells failed to rescue cisplatin or mitomycin sensitivity. Live-cell imaging demonstrated a significantly compromised recruitment of FANCJ-R707C to laser-induced DNA damage. However, FANCJ-R707C expressed in fancj-/- cells conferred resistance to the DNA polymerase inhibitor aphidicolin, G-quadruplex ligand telomestatin, or DNA strand-breaker bleomycin, whereas FANCJ-H396D failed. Thus, a minimal threshold of FANCJ catalytic activity is required to overcome replication stress induced by aphidicolin or telomestatin, or to repair bleomycin-induced DNA breakage. These findings have implications for therapeutic strategies relying on DNA cross-link sensitivity or heightened replication stress characteristic of cancer cells.
Collapse
Affiliation(s)
- Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Sanket Awate
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Irfan Khan
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Lynda Bradley
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graeme A King
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Takuye Abe
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Koji Kobayashi
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST) 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroyuki Kitao
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Dana Branzei
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224, USA
| |
Collapse
|
32
|
Oda S, Nomura S, Nakagawa M, Shin-Ya K, Kagaya N, Kawahara T. Solid-liquid Interface Screening SystemーApplication to the Screening of Antibiotic and Cytotoxic Substance-producing Fungi. Biocontrol Sci 2019; 24:47-56. [PMID: 30880313 DOI: 10.4265/bio.24.47] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
A useful tool for the screening of fungi producing biologically active secondary metabolites such as antibiotics and cytotoxic substances has been developed. An agar plate-organic solvent interface cultivation (A/S-IFC) system, which comprised a hydrophobic organic solvent (upper phase) , a fungal mat (middle phase) and an agar plate (lower phase) , was constructed. The metabolite profiles were compared among the A/S-IFC, a traditional submerged cultivation (SmC) and an extractive liquid surface immobilization (Ext-LSI) system consisted of a hydrophobic solvent (upper phase) , a fungal cells-ballooned microspheres (middle phase) and a liquid medium (lower phase) , with high-performance liquid chromatography-photodiode array detector (HPLC-PDA) . In the A/S-IFC, many hydrophobic metabolites vastly different from those in the SmC were accumulated in the organic phase as with the Ext-LSI. For example, a valuable azaphilone, sclerotiorin, was remarkably produced into the organic phase in the A/S-IFC. The A/S-IFC was applied to the screening of antibiotic-producing fungi. As a result of paper disk method, it was found that 321 isolated among 811 strains produced antifungal metabolites (hit rate, 39.6%) . Furthermore, 8, 23, and 30 strains also produced cytotoxic metabolites against SKOV-3 (human ovary adenocarcinoma) , MESO-1 (human malignant pleural mesothelioma) , and Jurkat cells (immortalized human T lymphocyte) .
Collapse
Affiliation(s)
- Shinobu Oda
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology.,Integrated Technology Research Center of Medicinal Science and Engineering, Kanazawa Institute of Technology
| | - Seiya Nomura
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology
| | - Manami Nakagawa
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science andTechnology (AIST)
| | - Noritaka Kagaya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science andTechnology (AIST)
| | - Teppei Kawahara
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science andTechnology (AIST).,Faculty of Life Science, Kumamoto University
| |
Collapse
|
33
|
Takami H, Toyoda A, Uchiyama I, Itoh T, Takaki Y, Arai W, Nishi S, Kawai M, Shin-Ya K, Ikeda H. Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1. DNA Res 2018; 24:169-177. [PMID: 28065880 PMCID: PMC5397603 DOI: 10.1093/dnares/dsw055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 06/14/2016] [Accepted: 11/19/2016] [Indexed: 11/13/2022] Open
Abstract
Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture. Thus, the strain was found more valuable than hitherto considered. In addition, M497-1 harbours 98 genes involved in the biosynthesis of various natural products, 16 of which are M497-1-specific across 4 Lysobacter species. A gene cluster starting at LEN_2603 through LEN_2673 among the 98 genes closely resembled the lysobactin biosynthesis gene cluster of Lysobacter sp. ATCC 53042. It is likely that M497-1 may produce lysobactin or related antibacterial compounds. Furthermore, comparative genomic analysis of M497-1 and four other Lysobacter species revealed that their core genome structure comprises 3,737 orthologous groups. Our findings are expected to advance further biotechnological application of Lysobacter spp. as a promising source of natural bioactive compounds.
Collapse
Affiliation(s)
- Hideto Takami
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Wataru Arai
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Shinro Nishi
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Mikihiko Kawai
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
| |
Collapse
|
34
|
Kawahara T, Izumikawa M, Kozone I, Hashimoto J, Kagaya N, Koiwai H, Komatsu M, Fujie M, Sato N, Ikeda H, Shin-Ya K. Neothioviridamide, a Polythioamide Compound Produced by Heterologous Expression of a Streptomyces sp. Cryptic RiPP Biosynthetic Gene Cluster. J Nat Prod 2018; 81:264-269. [PMID: 29381067 DOI: 10.1021/acs.jnatprod.7b00607] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During genome mining for thioviridamide-like biosynthetic gene clusters that could produce polythioamide RiPP (ribosomally synthesized and post-translationally modified peptides), we discovered a novel cryptic biosynthetic gene cluster. During efforts to express this biosynthetic gene using heterologous expression of this biosynthetic gene cluster, a novel compound designated as neothioviridamide was produced. We report herein the cloning and heterologous expression of the neothioviridamide biosynthetic gene cluster and the isolation, structure determination, and cytotoxic activity of neothioviridamide.
Collapse
Affiliation(s)
- Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hanae Koiwai
- Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato Sagamihara, Kanagawa 228-8555, Japan
| | - Mamoru Komatsu
- Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato Sagamihara, Kanagawa 228-8555, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Noriyuki Sato
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato Sagamihara, Kanagawa 228-8555, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- The Biotechnology Research Center, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
35
|
Niikura H, Maruyama C, Ogasawara Y, Shin-Ya K, Dairi T, Hamano Y. Functional analysis of methyltransferases participating in streptothricin-related antibiotic biosynthesis. J Biosci Bioeng 2017; 125:148-154. [PMID: 29029816 DOI: 10.1016/j.jbiosc.2017.09.004] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/05/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
Abstract
Streptothricin (ST) and its related compounds produced by Streptomyces strains are broad-spectrum antibiotics that consist of carbamoylated d-gulosamine, amino-acid side chain, and streptolidine lactam moieties. BD-12, a streptothricin-related antibiotic, has a glycine-derived side chain and two N-methyl groups, whereas ST-F carrying the l-β-lysine side chain has no methyl group. In our previous studies, we identified and characterized the BD-12 and ST biosynthetic gene clusters. Here we report the functional analysis of two methyltransferase genes (orf 6 and orf 13) in the BD-12 biosynthetic gene cluster. Combinatorial biosynthesis using these two methyltransferase genes and the ST biosynthetic gene cluster resulted in the production of three methylated forms of ST-F. Among them, N,N'-dimethyl-ST-F, a novel compound generated in the present study, showed bacteria-specific antibiotic activities, although ST-F exhibits antibiotic activities against both prokaryotes and eukaryotes. Our findings also demonstrated that the orf 6 and orf 13 genes are responsible for the N-methylations of the amide bonds in the streptolidine lactam and in the amino-acid side chain linkage, respectively, and that N-methyl modification of the streptolidine lactam confers resistance in part against an ST hydrolase, SttH.
Collapse
Affiliation(s)
- Haruka Niikura
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui 910-1195, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui 910-1195, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan; The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui 910-1195, Japan.
| |
Collapse
|
36
|
Ito S, Ogawa K, Takeuchi K, Takagi M, Yoshida M, Hirokawa T, Hirayama S, Shin-Ya K, Shimada I, Doi T, Goshima N, Natsume T, Nagata K. A small-molecule compound inhibits a collagen-specific molecular chaperone and could represent a potential remedy for fibrosis. J Biol Chem 2017; 292:20076-20085. [PMID: 29025875 DOI: 10.1074/jbc.m117.815936] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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: 09/02/2017] [Revised: 10/10/2017] [Indexed: 11/06/2022] Open
Abstract
Fibrosis can disrupt tissue structure and integrity and impair organ function. Fibrosis is characterized by abnormal collagen accumulation in the extracellular matrix. Pharmacological inhibition of collagen secretion therefore represents a promising strategy for the management of fibrotic disorders, such as liver and lung fibrosis. Hsp47 is an endoplasmic reticulum (ER)-resident collagen-specific molecular chaperone essential for correct folding of procollagen in the ER. Genetic deletion of Hsp47 or inhibition of its interaction with procollagen interferes with procollagen triple helix production, which vastly reduces procollagen secretion from fibroblasts. Thus, Hsp47 could be a potential and promising target for the management of fibrosis. In this study, we screened small-molecule compounds that inhibit the interaction of Hsp47 with collagen from chemical libraries using surface plasmon resonance (BIAcore), and we found a molecule AK778 and its cleavage product Col003 competitively inhibited the interaction and caused the inhibition of collagen secretion by destabilizing the collagen triple helix. Structural information obtained with NMR analysis revealed that Col003 competitively binds to the collagen-binding site on Hsp47. We propose that these structural insights could provide a basis for designing more effective therapeutic drugs for managing fibrosis.
Collapse
Affiliation(s)
- Shinya Ito
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555; Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507
| | - Koji Ogawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064
| | - Koh Takeuchi
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064
| | - Masahito Yoshida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578
| | - Takatsugu Hirokawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064
| | | | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064
| | - Ichio Shimada
- Division of Physical Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578
| | - Naoki Goshima
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064
| | - Tohru Natsume
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064.
| | - Kazuhiro Nagata
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555; Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kyoto 603-8555, Japan.
| |
Collapse
|
37
|
Amagai K, Ikeda H, Hashimoto J, Kozone I, Izumikawa M, Kudo F, Eguchi T, Nakamura T, Osada H, Takahashi S, Shin-Ya K. Identification of a gene cluster for telomestatin biosynthesis and heterologous expression using a specific promoter in a clean host. Sci Rep 2017; 7:3382. [PMID: 28611443 PMCID: PMC5469769 DOI: 10.1038/s41598-017-03308-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/26/2017] [Indexed: 01/24/2023] Open
Abstract
Telomestatin, a strong telomerase inhibitor with G-quadruplex stabilizing activity, is a potential therapeutic agent for treating cancers. Difficulties in isolating telomestatin from microbial cultures and in chemical synthesis are bottlenecks impeding the wider use. Therefore, improvement in telomestatin production and structural diversification are required for further utilization and application. Here, we discovered the gene cluster responsible for telomestatin biosynthesis, and achieved production of telomestatin by heterologous expression of this cluster in the engineered Streptomyces avermitilis SUKA strain. Utilization of an optimal promoter was essential for successful production. Gene disruption studies revealed that the tlsB, tlsC, and tlsO-T genes play key roles in telomestatin biosynthesis. Moreover, exchanging TlsC core peptide sequences resulted in the production of novel telomestatin derivatives. This study sheds light on the expansion of chemical diversity of natural peptide products for drug development.
Collapse
Affiliation(s)
- Keita Amagai
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Takemichi Nakamura
- RIKEN Center for Sustainable Resource Science, Molecular Structure Characterization Unit, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
| |
Collapse
|
38
|
Miyanaga A, Hayakawa Y, Numakura M, Hashimoto J, Teruya K, Hirano T, Shin-Ya K, Kudo F, Eguchi T. Identification of the Fluvirucin B2 (Sch 38518) Biosynthetic Gene Cluster from Actinomadura fulva subsp. indica ATCC 53714: substrate Specificity of the β-Amino Acid Selective Adenylating Enzyme FlvN. Biosci Biotechnol Biochem 2016; 80:935-41. [PMID: 26818633 DOI: 10.1080/09168451.2015.1132155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluvirucins are 14-membered macrolactam polyketides that show antifungal and antivirus activities. Fluvirucins have the β-alanine starter unit at their polyketide skeletons. To understand the construction mechanism of the β-alanine moiety in fluvirucin biosyntheses, we have identified the biosynthetic cluster of fluvirucin B2 produced from Actinomadura fulva subsp. indica ATCC 53714. The identified gene cluster contains three polyketide synthases, four characteristic β-amino acid-carrying enzymes, one decarboxylase, and one amidohydrolase. We next investigated the activity of the adenylation enzyme FlvN, which is a key enzyme for the selective incorporation of a β-amino acid substrate. FlvN showed strong preference for l-aspartate over other amino acids such as β-alanine. Based on these results, we propose a biosynthetic pathway for fluvirucin B2.
Collapse
Affiliation(s)
- Akimasa Miyanaga
- a Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | - Yuki Hayakawa
- b Department of Chemistry and Materials Science , Tokyo Institute of Technology , Tokyo , Japan
| | - Mario Numakura
- a Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | | | - Kuniko Teruya
- d Okinawa Biotechnology Business Support Center , Okinawa Institute of Advanced Sciences , Uruma , Japan
| | - Takashi Hirano
- d Okinawa Biotechnology Business Support Center , Okinawa Institute of Advanced Sciences , Uruma , Japan.,e Okinawa Biotechnology Business Support Center , Okinawa Science and Technology Promotion Center , Uruma , Japan
| | - Kazuo Shin-Ya
- f National Institute of Advanced Industrial Science and Technology , Tokyo , Japan
| | - Fumitaka Kudo
- a Department of Chemistry , Tokyo Institute of Technology , Tokyo , Japan
| | - Tadashi Eguchi
- b Department of Chemistry and Materials Science , Tokyo Institute of Technology , Tokyo , Japan
| |
Collapse
|
39
|
Ohno S, Katsuyama Y, Tajima Y, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-Ya K, Ohnishi Y. Identification and Characterization of the Streptazone E Biosynthetic Gene Cluster in Streptomyces sp. MSC090213JE08. Chembiochem 2015; 16:2385-91. [PMID: 26403163 DOI: 10.1002/cbic.201500317] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 06/24/2015] [Indexed: 11/10/2022]
Abstract
Streptazone derivatives isolated from Streptomyces species are piperidine alkaloids with a cyclopenta[b]pyridine scaffold. Previous studies indicated that these compounds are polyketides, but the biosynthetic enzymes responsible for their synthesis are unknown. Here, we have identified the streptazone E biosynthetic gene cluster in Streptomyces sp. MSC090213JE08, which encodes a modular type I PKS and tailoring enzymes that include an aminotransferase, three oxidoreductases, and two putative cyclases. The functions of the six tailoring enzymes were analyzed by gene disruption, and two putative biosynthetic intermediates that accumulated in particular mutants were structurally elucidated. On the basis of these results, we propose a pathway for the biosynthesis of streptazone E in which the two putative cyclases of the nuclear transport factor 2-like superfamily are responsible for C-C bond formation coupled with epoxide ring opening to give the five-membered ring of streptazone E.
Collapse
Affiliation(s)
- Shoto Ohno
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuka Tajima
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
40
|
Moriya C, Hosoya T, Agawa S, Sugiyama Y, Kozone I, Shin-Ya K, Terahara N, Kumazawa S. New acylated anthocyanins from purple yam and their antioxidant activity. Biosci Biotechnol Biochem 2015; 79:1484-92. [PMID: 25848974 DOI: 10.1080/09168451.2015.1027652] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 10/23/2022]
Abstract
Purple yam (Dioscorea alata L.), which is widely distributed in tropical and subtropical regions, is characterized by its color and viscosity. Previous studies have shown that purple yams contain a variety of acylated anthocyanins that exhibit higher levels of antioxidant activity than the corresponding nonacylated compounds. In this study, the pigments found in purple yams from the Philippines (D. alata) were isolated and evaluated in terms of antioxidant activity. Four new acylated anthocyanins, alanins (1-4) were isolated from the MeOH extracts of purple yam, which were subsequently determined to be cyanidin (1, 2, and 4) and peonidin (3) type compounds, along with four known anthocyanins (5-8). The structures of 1-4 were determined by spectroscopic methods, including NMR and MS analyses. The antioxidant activities of anthocyanins 1-8 were investigated using oxygen radical absorbing capacity and ferric reducing antioxidant power assays.
Collapse
Affiliation(s)
- Chiemi Moriya
- a Department of Food and Nutritional Sciences , University of Shizuoka , Shizuoka , Japan
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Abstract
Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes.
Collapse
Affiliation(s)
- Yuuki Yamada
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan
| | - Mamoru Komatsu
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Satoshi Omura
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108-8461, Japan; and
| | - David E Cane
- Department of Chemistry, Brown University, Providence, RI 02912-9108
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan;
| |
Collapse
|
42
|
Izumikawa M, Itoh M, Kawahara T, Sakata N, Tsuchida T, Mizukami T, Shin-Ya K. A highly oxygenated ergostane--MBJ-0005--from Anthostomella eucalyptorum f25427. J Antibiot (Tokyo) 2014; 67:843-5. [PMID: 24961710 DOI: 10.1038/ja.2014.82] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/21/2014] [Accepted: 06/02/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Masashi Itoh
- Bioresource Laboratories, MicroBiopharm Japan Co., Ltd. (MBJ), Shizuoka, Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | - Noriaki Sakata
- Bioresource Laboratories, MicroBiopharm Japan Co., Ltd. (MBJ), Shizuoka, Japan
| | - Toshio Tsuchida
- Bioresource Laboratories, MicroBiopharm Japan Co., Ltd. (MBJ), Shizuoka, Japan
| | - Tamio Mizukami
- Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| |
Collapse
|
43
|
Shin-Ya K. Novel Antitumor and Neuroprotective Substances Discovered by Characteristic Screenings Based on Specific Molecular Targets. Biosci Biotechnol Biochem 2014; 69:867-72. [PMID: 15914903 DOI: 10.1271/bbb.69.867] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 11/08/2022]
Abstract
In the course of characteristic screening for antitumor substances, we isolated novel inhibitors against telomerase and the expression of molecular chaperone GRP78, designated telomestatin and versipelostatin, respectively. Telomestatin specifically acts on telomere sequence to stabilize the specific DNA structure called G-quadruplex and shows unique biological aspects that induce telomere dysfunction. Versipelostatin decreased the expression of GRP78 accompanied by a high level of cell death under glucose deprived conditions that mimicked the circumstances of a solid tumor. Furthermore, a screening program for glutamate receptor antagonist to treat brain stroke resulted in the isolation of an AMPA/NMDA antagonist kaitocephalin. Kaitocephalin potently protected rat hippocampal neurons from kainate, AMPA, and NMDA excitotoxicity. It also inhibited the Ca(2+) influx elicited by AMPA and NMDA, but not by kainate. Detailed analysis for the mode of action mechanism of these compounds indicated novel and unique biological phenomena not revealed by molecular biological techniques.
Collapse
Affiliation(s)
- Kazuo Shin-Ya
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
44
|
Kawahara T, Itoh M, Izumikawa M, Sakata N, Tsuchida T, Shin-Ya K. Novel aziridine-containing peptides MBJ-0034 and MBJ-0035 from Streptosporangium sp. 32552. J Antibiot (Tokyo) 2014; 67:577-80. [PMID: 24619229 DOI: 10.1038/ja.2014.19] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, Japan
| | - Masashi Itoh
- Bioresource Laboratories, MicroBiopharm Japan Co., Ltd. (MBJ), Iwata, Shizuoka, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, Japan
| | - Noriaki Sakata
- Bioresource Laboratories, MicroBiopharm Japan Co., Ltd. (MBJ), Iwata, Shizuoka, Japan
| | - Toshio Tsuchida
- Bioresource Laboratories, MicroBiopharm Japan Co., Ltd. (MBJ), Iwata, Shizuoka, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| |
Collapse
|
45
|
Lin W, Sampathi S, Dai H, Liu C, Zhou M, Hu J, Huang Q, Campbell J, Shin-Ya K, Zheng L, Chai W, Shen B. Mammalian DNA2 helicase/nuclease cleaves G-quadruplex DNA and is required for telomere integrity. EMBO J 2013; 32:1425-39. [PMID: 23604072 DOI: 10.1038/emboj.2013.88] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/26/2013] [Indexed: 01/23/2023] Open
Abstract
Efficient and faithful replication of telomeric DNA is critical for maintaining genome integrity. The G-quadruplex (G4) structure arising in the repetitive TTAGGG sequence is thought to stall replication forks, impairing efficient telomere replication and leading to telomere instabilities. However, pathways modulating telomeric G4 are poorly understood, and it is unclear whether defects in these pathways contribute to genome instabilities in vivo. Here, we report that mammalian DNA2 helicase/nuclease recognizes and cleaves telomeric G4 in vitro. Consistent with DNA2's role in removing G4, DNA2 deficiency in mouse cells leads to telomere replication defects, elevating the levels of fragile telomeres (FTs) and sister telomere associations (STAs). Such telomere defects are enhanced by stabilizers of G4. Moreover, DNA2 deficiency induces telomere DNA damage and chromosome segregation errors, resulting in tetraploidy and aneuploidy. Consequently, DNA2-deficient mice develop aneuploidy-associated cancers containing dysfunctional telomeres. Collectively, our genetic, cytological, and biochemical results suggest that mammalian DNA2 reduces replication stress at telomeres, thereby preserving genome stability and suppressing cancer development, and that this may involve, at least in part, nucleolytic processing of telomeric G4.
Collapse
Affiliation(s)
- Weiqiang Lin
- Department of Radiation Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Kobayashi H, Harada H, Nakamura M, Futamura Y, Ito A, Yoshida M, Iemura SI, Shin-Ya K, Doi T, Takahashi T, Natsume T, Imoto M, Sakakibara Y. Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications. BMC Chem Biol 2012; 12:2. [PMID: 22480302 PMCID: PMC3471015 DOI: 10.1186/1472-6769-12-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/05/2012] [Indexed: 12/14/2022]
Abstract
Background Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis. Results We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system. As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins. Conclusions This study revealed that our proposed protocol of predicting target protein combining in silico screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.
Collapse
Affiliation(s)
- Hiroki Kobayashi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Hiroko Harada
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Masaomi Nakamura
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Yushi Futamura
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Akihiro Ito
- Chemical Genetics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Shun-Ichiro Iemura
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Takashi Takahashi
- Department of Applied Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo, 152-8552, Japan
| | - Tohru Natsume
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Masaya Imoto
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| |
Collapse
|
47
|
Abstract
The search for metabolites of Kibdelosporangium sp. AK-AA56 resulted in the discovery of novel N-phenylacetylated peptides, JBIR-78 (1) and JBIR-95 (2). Compounds 1 and 2 were established to be N-phenylacetylated heptapeptides by extensive NMR and HRESIMS analyses. The absolute configuration of the standard amino acids including a cysteic acid moiety was determined using Marfey's method on the acid hydrolysates of 1 and 2. The relative and absolute configurations of a nonstandard amino acid, β-hydroxyleucine, were elucidated using the J-based and modified Mosher's methods, respectively. In an antimicrobial test, 1 showed antibacterial activity against Micrococcus luteus.
Collapse
Affiliation(s)
- Miho Izumikawa
- Biomedicinal Information Research Center (BIRC), Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | | | | |
Collapse
|
48
|
Ohnuki S, Kobayashi T, Ogawa H, Kozone I, Ueda JY, Takagi M, Shin-Ya K, Hirata D, Nogami S, Ohya Y. Analysis of the biological activity of a novel 24-membered macrolide JBIR-19 in Saccharomyces cerevisiae by the morphological imaging program CalMorph. FEMS Yeast Res 2012; 12:293-304. [PMID: 22129199 DOI: 10.1111/j.1567-1364.2011.00770.x] [Citation(s) in RCA: 22] [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] [Received: 09/27/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 11/29/2022] Open
Abstract
To investigate the biological activity of a novel 24-membered macrolide compound, JBIR-19, isolated from the culture broth of the entomopathogenic fungus Metarhizium sp. fE61, morphological changes in yeast cells were examined using the automated image-processing program CalMorph. Principal components analysis was used to elucidate dynamic changes in the phenotypes, revealing two independent effects of JBIR-19 in yeast cells: bud elongation and increased size of the actin region. Using a fitness assay, we identified the genes required for robust growth in the presence of JBIR-19. Among these were CCW12, YLR111W, and DHH1, which are also involved in abnormal bud morphology. Based on these results and others, we predict intracellular targets of JBIR-19 and its functional interactions.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Rosu F, Gabelica V, Smargiasso N, Mazzucchelli G, Shin-Ya K, De Pauw E. Cation involvement in telomestatin binding to g-quadruplex DNA. J Nucleic Acids 2010; 2010. [PMID: 20700418 PMCID: PMC2911584 DOI: 10.4061/2010/121259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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: 02/01/2010] [Accepted: 04/13/2010] [Indexed: 11/20/2022] Open
Abstract
The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show the incorporation of one extra ammonium ion in the telomestatin complexes. Experiments on telomestatin alone also show that the telomestatin alone is able to coordinate cations in a similar way as a crown ether. Finally, density functional theory calculations suggest that in the G-quadruplex-telomestatin complex, potassium or ammonium cations are located between the telomestatin and a G-quartet. This study underlines that monovalent cation coordination capabilities should be integrated in the rational design of G-quadruplex binding ligands.
Collapse
Affiliation(s)
- Frédéric Rosu
- Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, 4000 Liège, Belgium
| | | | | | | | | | | |
Collapse
|
50
|
Iida K, Tera M, Hirokawa T, Shin-Ya K, Nagasawa K. Synthesis of Macrocyclic Hexaoxazole (6OTD) Dimers, Containing Guanidine and Amine Functionalized Side Chains, and an Evaluation of Their Telomeric G4 Stabilizing Properties. J Nucleic Acids 2010; 2010. [PMID: 20700415 PMCID: PMC2911606 DOI: 10.4061/2010/217627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [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: 02/15/2010] [Accepted: 03/01/2010] [Indexed: 12/03/2022] Open
Abstract
Structure-activity relationship studies were carried out on macrocyclic hexaoxazole (6OTD) dimers, whose core structure stabilizes telomeric G-quadruplexes (G4). Two new 6OTD dimers having side chain amine and guanidine functional groups were synthesized and evaluated for their stabilizing ability against a telomeric G4 DNA sequence. The results show that the 6OTD dimers interact with the DNA to form 1:1 complexes and stabilize the antiparallel G4 structure of DNA in the presence of potassium cation. The guanidine functionalized dimer displays a potent stabilizing ability of the G4 structure, as determined by using a FRET melting assay (ΔTm = 14°C).
Collapse
Affiliation(s)
- Keisuke Iida
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo 184-8588, Japan
| | | | | | | | | |
Collapse
|