1
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Siddika MA, Oi H, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes. Molecules 2023; 28:6465. [PMID: 37764241 PMCID: PMC10535472 DOI: 10.3390/molecules28186465] [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: 08/05/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The multimolecular assembly of three-dimensionally structured proteins forms their quaternary structures, some of which have high geometric symmetry. The size and complexity of protein quaternary structures often increase in a hierarchical manner, with simpler, smaller structures serving as units for larger quaternary structures. In this study, we exploited oligomerization of a ribozyme cyclic trimer to achieve larger ribozyme-based RNA assembly. By installing kissing loop (KL) interacting units to one-, two-, or three-unit RNA molecules in the ribozyme trimer, we constructed dimers, open-chain oligomers, and branched oligomers of ribozyme trimer units. One type of open-chain oligomer preferentially formed a closed tetramer containing 12 component RNAs to provide 12 ribozyme units. We also observed large assembly of ribozyme trimers, which reached 1000 nm in size.
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Affiliation(s)
- Mst. Ayesha Siddika
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Toyama, Japan (S.M.)
| | - Hiroki Oi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8501, Kyoto, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Kyoto, Japan; (H.S.); (M.E.)
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Kyoto, Japan; (H.S.); (M.E.)
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita 564-8680, Osaka, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Toyama, Japan (S.M.)
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Toyama, Japan (S.M.)
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
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2
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Ueda T, Nishimura KI, Nishiyama Y, Tominaga Y, Miyazaki K, Furuta H, Matsumura S, Ikawa Y. Pairwise Engineering of Tandemly Aligned Self-Splicing Group I Introns for Analysis and Control of Their Alternative Splicing. Biomolecules 2023; 13:biom13040654. [PMID: 37189401 DOI: 10.3390/biom13040654] [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] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Alternative splicing is an important mechanism in the process of eukaryotic nuclear mRNA precursors producing multiple protein products from a single gene. Although group I self-splicing introns usually perform regular splicing, limited examples of alternative splicing have also been reported. The exon-skipping type of splicing has been observed in genes containing two group I introns. To characterize splicing patterns (exon-skipping/exon-inclusion) of tandemly aligned group I introns, we constructed a reporter gene containing two Tetrahymena introns flanking a short exon. To control splicing patterns, we engineered the two introns in a pairwise manner to design pairs of introns that selectively perform either exon-skipping or exon-inclusion splicing. Through pairwise engineering and biochemical characterization, the structural elements important for the induction of exon-skipping splicing were elucidated.
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Affiliation(s)
- Tomoki Ueda
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kei-ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuka Nishiyama
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yuto Tominaga
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Katsushi Miyazaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
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3
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Siddika MA, Yamada T, Aoyama R, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes. Molecules 2022; 27:molecules27238298. [PMID: 36500390 PMCID: PMC9740620 DOI: 10.3390/molecules27238298] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
Naturally occurring ribozymes with a modular architecture are promising platforms for construction of RNA nanostructures because modular redesign enables their oligomerization. The resulting RNA nanostructures can exhibit the catalytic function of the parent ribozyme in an assembly dependent manner. In this study, we designed and constructed open-form oligomers of a bimolecular form of an RNase P ribozyme. The ribozyme oligomers were analyzed biochemically and by atomic force microscopy (AFM).
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Affiliation(s)
- Mst. Ayesha Siddika
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Takahiro Yamada
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Risako Aoyama
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kumi Hidaka
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Osaka 564-8680, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Correspondence:
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4
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Hatakeyama M, Yamamoto T, Yasuda K, Matsumura S, Yasunaga K, Sato K. In-situ Observation of Damage Structure in Cu-Cr-Zr and Cu-Cr Alloy During 1.25 MeV Electron Irradiation. Nuclear Materials and Energy 2022. [DOI: 10.1016/j.nme.2022.101144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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6
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Dobirul Islam M, Motiar Rahman M, Matsumura S, Ikawa Y. Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module. Nucleosides Nucleotides Nucleic Acids 2021; 40:867-883. [PMID: 34402751 DOI: 10.1080/15257770.2021.1956531] [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] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
While current group I ribozymes use several distinct strategies to function under conditions of low Mg2+ concentration (≤ 3 mM), a deletion mutant of the Tetrahymena ribozyme (ΔP5 ribozyme) is virtually inactive with 3 mM Mg2+ due to removal of the large peripheral module, P5abc, supporting the active conformation of the core module. We investigated the molecular crowding effects of synthetic polyethylene glycols (PEGs) on the activity of the ΔP5 ribozyme. Among PEG molecules with different chain lengths, PEG600 improved the activity of the ΔP5 ribozyme most effectively in the presence of 3 mM Mg2+.
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Affiliation(s)
- Md Dobirul Islam
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Md Motiar Rahman
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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7
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Yokoyama S, Fujita Y, Matsumura S, Yoshimura T, Kinoshita I, Watanabe T, Tabata H, Tsuji T, Ozawa S, Tamaki T, Nakatani Y, Oka M. Cribriform carcinoma in the lymph nodes is associated with distant metastasis, recurrence, and survival among patients with node-positive colorectal cancer. Br J Surg 2021; 108:e111-e112. [PMID: 33793704 DOI: 10.1093/bjs/znaa123] [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] [Received: 10/12/2020] [Accepted: 11/15/2020] [Indexed: 11/13/2022]
Abstract
Cribriform lymph node pattern is an independent risk factor for metachronous or synchronous distant metastasis in patients with stage III and IV node-positive colorectal cancer. Multivariable analysis in patients with stage III disease indicated that the cribriform pattern of carcinoma in the lymph nodes was an independent risk factor for recurrence and survival. Kaplan–Meier analysis demonstrated that the group with stage III cribriform-type lymph node carcinoma had shorter recurrence-free and overall survival times than the stage III group with the tubular type (P < 0.001).
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Affiliation(s)
- S Yokoyama
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - Y Fujita
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - S Matsumura
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - T Yoshimura
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - I Kinoshita
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - T Watanabe
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - H Tabata
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - T Tsuji
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - S Ozawa
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - T Tamaki
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - Y Nakatani
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
| | - M Oka
- Department of Surgery, National Hospital Organization Minami Wakayama Medical Centre, Wakayama, Japan
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8
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Abe Y, Matsumura S. Ihe Relationship between Defoaming Power and Dynamic Surface Tension of Sodium Dodecylbenzene Sulfonate Solutions with Alcohols. TENSIDE SURFACT DET 2021. [DOI: 10.1515/tsd-1983-200503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Mori Y, Oi H, Suzuki Y, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Flexible Assembly of Engineered Tetrahymena Ribozymes Forming Polygonal RNA Nanostructures with Catalytic Ability. Chembiochem 2021; 22:2168-2176. [PMID: 33876531 DOI: 10.1002/cbic.202100109] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Indexed: 11/11/2022]
Abstract
Ribozymes with modular architecture constitute an attractive class of structural platforms for design and construction of nucleic acid nanostructures with biological functions. Through modular engineering of the Tetrahymena ribozyme, we have designed unit RNAs (L-RNAs), assembly of which formed ribozyme-based closed trimers and closed tetramers. Their catalytic activity was dependent on oligomer formation. In this study, the structural variety of L-RNA oligomers was extended by tuning their structural elements, yielding closed pentamers and closed hexamers. Their assembly properties were analyzed by electrophoretic mobility shift assay (EMSA) and atomic force microscopy (AFM).
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Affiliation(s)
- Yuki Mori
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Hiroki Oi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, 606-8502, Kyoto, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, 930-8555, Toyama, Japan
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10
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Suzuki H, Ueda N, Matsumura S, Masui M, Tsutsumi C, Mori M, Okubo Y, Ishiguro K. 246P A survey of breast cancer patients’ attitudes toward the breast reconstruction based on breast implant associated-anaplastic large cell lymphoma (BIA-ALCL). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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11
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Kiyooka R, Akagi J, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures. J Biosci Bioeng 2020; 130:253-259. [PMID: 32451246 DOI: 10.1016/j.jbiosc.2020.04.010] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022]
Abstract
Ribozymes with modular structures are attractive platforms for the construction of nanoscale RNA objects with biological functions. We designed group I ribozyme dimers as unit ribozyme dimers (Urds), which self-assembled to form their polymeric states and also oligomeric states with defined numbers of Urds. Assembly of Urds yielded catalytic ability of a pair of distinct ribozyme units to cleave two distinct substrates. The morphologies of the assembled ribozyme structures were observed directly by atomic force microscopy (AFM).
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Affiliation(s)
- Ryuji Kiyooka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Junya Akagi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
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12
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Rahman MS, Matsumura S, Ikawa Y. Effects of external molecular factors on adaptation of bacterial RNase P ribozymes to thermophilic conditions. Biochem Biophys Res Commun 2020; 523:342-347. [DOI: 10.1016/j.bbrc.2019.12.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/12/2019] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
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13
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Rahman MS, Gulshan MA, Matsumura S, Ikawa Y. Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes. Nucleosides Nucleotides Nucleic Acids 2020; 39:715-729. [PMID: 32039645 DOI: 10.1080/15257770.2019.1687909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures of precursor tRNAs (pre-tRNAs) to cleave their 5' leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA and C-domain RNA assemble to form bimolecular forms of RNase P ribozymes. We analyzed the effects of polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by bimolecular RNase P ribozymes to examine the effects of molecular crowding on the reaction. PEG molecular crowders significantly enhanced the activities of bimolecular RNase P ribozymes, some of which were hardly active without PEGs.
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Affiliation(s)
- Md Sohanur Rahman
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Mst Ara Gulshan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
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14
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Tsuruga R, Uehara N, Suzuki Y, Furuta H, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA–RNA interface between two structural modules. J Biosci Bioeng 2019; 128:410-415. [DOI: 10.1016/j.jbiosc.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
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15
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Nozawa Y, Hagihara M, Rahman MS, Matsumura S, Ikawa Y. Rational Design of an Orthogonal Pair of Bimolecular RNase P Ribozymes through Heterologous Assembly of Their Modular Domains. Biology (Basel) 2019; 8:biology8030065. [PMID: 31480450 PMCID: PMC6783828 DOI: 10.3390/biology8030065] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 12/14/2022]
Abstract
The modular structural domains of multidomain RNA enzymes can often be dissected into separate domain RNAs and their noncovalent assembly can often reconstitute active enzymes. These properties are important to understand their basic characteristics and are useful for their application to RNA-based nanostructures. Bimolecular forms of bacterial RNase P ribozymes consisting of S-domain and C-domain RNAs are attractive as platforms for catalytic RNA nanostructures, but their S-domain/C-domain assembly was not optimized for this purpose. Through analysis and engineering of bimolecular forms of the two bacterial RNase P ribozymes, we constructed a chimeric ribozyme with improved catalytic ability and S-domain/C-domain assembly and developed a pair of bimolecular RNase P ribozymes the assembly of which was considerably orthogonal to each other.
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Affiliation(s)
- Yuri Nozawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Megumi Hagihara
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Md Sohanur Rahman
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
- Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
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16
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Nozawa Y, Hagihara M, Matsumura S, Ikawa Y. Modular Architecture of Bacterial RNase P Ribozymes as a Structural Platform for RNA Nanostructure Design. Chimia (Aarau) 2018; 72:882-887. [DOI: 10.2533/chimia.2018.882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yuri Nozawa
- Department of Chemistry Graduate School of Science and Engineering University of Toyama Gofuku 3190, Toyama, Japan
| | - Megumi Hagihara
- Department of Chemistry Graduate School of Science and Engineering University of Toyama Gofuku 3190, Toyama, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry Graduate School of Science and Engineering University of Toyama Gofuku 3190, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry Graduate School of Science and Engineering University of Toyama Gofuku 3190, Toyama, Japan;,
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17
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Rahman MM, Matsumura S, Ikawa Y. Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers. Biochem Biophys Res Commun 2018; 507:136-141. [DOI: 10.1016/j.bbrc.2018.10.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 01/04/2023]
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18
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Gulshan MA, Tsuji K, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Distinct modulation of group I ribozyme activity among stereoisomers of a synthetic pentamine with structural constraints. Biochem Biophys Res Commun 2018; 504:698-703. [PMID: 30213632 DOI: 10.1016/j.bbrc.2018.09.015] [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: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 11/25/2022]
Abstract
Among cationic molecules that can modulate ribozyme activities, polyamines act as both activator and inhibitor of ribozyme reactions partly due to their structural flexibility. Restriction of structural flexibility of polyamines may allow them to emphasize particular modulation effects. We examined eight stereoisomers of a synthetic pentamine bearing three cyclopentane rings. In the reaction of a structurally unstable group I ribozyme, three stereoisomers exhibited distinct effects as inhibitor, an additive with a neutral effect, and also as an activator.
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Affiliation(s)
- Mst Ara Gulshan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
| | - Kasumi Tsuji
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan.
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19
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Rahman MM, Matsumura S, Ikawa Y. Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site. J Mol Evol 2018; 86:431-442. [DOI: 10.1007/s00239-018-9862-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022]
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20
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Gulshan MA, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Comparative study of polyethylene polyamines as activator molecules for a structurally unstable group I ribozyme. Biosci Biotechnol Biochem 2018; 82:1404-1407. [PMID: 29699448 DOI: 10.1080/09168451.2018.1465811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Polyamines are a promising class of molecules that can modulate RNA enzyme activities. To analyze the effects of the number of amine moieties systematically, we employed four polyamines sharing dimethylene units to connect amine moieties. As a model RNA enzyme, we used a structurally unstable group I ribozyme, which was activated most and least efficiently by tetraethylenepentamine and diethylenetriamine respectively.
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Affiliation(s)
- Mst Ara Gulshan
- a Department of Chemistry, Graduate School of Science and Engineering , University of Toyama , Toyama , Japan.,b Graduate School of Innovative Life Science , University of Toyama , Toyama , Japan
| | - Shigeyoshi Matsumura
- a Department of Chemistry, Graduate School of Science and Engineering , University of Toyama , Toyama , Japan
| | - Tsunehiko Higuchi
- c Graduate School of Pharmaceutical Sciences , Nagoya City University , Nagoya , Japan
| | - Naoki Umezawa
- c Graduate School of Pharmaceutical Sciences , Nagoya City University , Nagoya , Japan
| | - Yoshiya Ikawa
- a Department of Chemistry, Graduate School of Science and Engineering , University of Toyama , Toyama , Japan
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21
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Inuzuka S, Kakizawa H, Nishimura KI, Naito T, Miyazaki K, Furuta H, Matsumura S, Ikawa Y. Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain. Genes Cells 2018; 23:435-447. [PMID: 29693296 DOI: 10.1111/gtc.12586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/18/2018] [Indexed: 12/31/2022]
Abstract
The riboswitch is a class of RNA-based gene regulatory machinery that is dependent on recognition of its target ligand by RNA tertiary structures. Ligand recognition is achieved by the aptamer domain, and ligand-dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. Ligand-dependent structural changes of the aptamer domain and expression platform have been reported for several riboswitches with short (<40 nucleotides) expression platforms. In this study, we characterized structural changes of the Vc2 c-di-GMP riboswitch that represses translation of downstream open reading frames in a ligand-dependent manner. The Vc2 riboswitch has a long (97 nucleotides) expression platform, but its structure and function are largely unknown. Through mutational analysis and chemical probing, we identified its secondary structures that are possibly responsible for switch-OFF and switch-ON states of translational initiation.
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Affiliation(s)
- Saki Inuzuka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Hitoshi Kakizawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Kei-Ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Takuto Naito
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Katsushi Miyazaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
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22
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Saida K, Kamei K, Ogura M, Matsumura S, Kano Y, Sato M, Andoh A, Ishikura K. Azathioprine-induced Agranulocytosis and Severe Alopecia After Kidney Transplantation Associated With a NUDT15 Polymorphism: A Case Report. Transplant Proc 2018; 50:3925-3927. [PMID: 30577288 DOI: 10.1016/j.transproceed.2018.04.039] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/12/2018] [Indexed: 01/17/2023]
Abstract
BACKGROUND Azathioprine (AZA) is the drug recommended for the continuation of immunosuppressive treatment after renal transplant in women during pregnancy. CASE REPORT A 37-year-old Japanese female developed agranulocytosis and severe alopecia after initiation of AZA (50 mg), used as an alternative to mycophenolate mofetil (MMF, 1000 mg) therapy in anticipation of a planned pregnancy. Within 4 days of the initiation of AZA therapy, the patient developed a high fever, leucopenia, and cranial alopecia. Genetic testing revealed a homozygous polymorphism of NUDT15 (rs116855232, NM_018283.3:c.415C>T: p.Arg139Cys), which has previously been identified as a risk factor for AZA-related complications in patients with inflammatory bowel disease. CONCLUSION Genetic screening for NUDT15 could contribute to the prevention of serious adverse reactions to AZA and provide the opportunity for personalized medicine. Identification of a safe alternative to MMF during pregnancy after a renal transplant is a problem to be resolved in the future.
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Affiliation(s)
- K Saida
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - K Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - M Ogura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - S Matsumura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Y Kano
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - M Sato
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - A Andoh
- Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | - K Ishikura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan.
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23
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Yoshioka S, Tsuruta K, Yamamoto T, Yasuda K, Matsumura S, Ishikawa N, Kobayashi E. X-ray absorption near edge structure and first-principles spectral investigations of cationic disorder in MgAl 2O 4 induced by swift heavy ions. Phys Chem Chem Phys 2018; 20:4962-4969. [PMID: 29387834 DOI: 10.1039/c7cp07591j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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
Cationic disorder in the MgAl2O4 spinel induced by swift heavy ions was investigated using the X-ray absorption near edge structure. With changes in the irradiation fluences of 200 MeV Xe ions, the Mg K-edge and Al K-edge spectra were synchronously changed. The calculated spectra based on density function theory indicate that the change in the experimental spectra was due to cationic disorder between Mg in tetrahedral sites and Al in octahedral sites. These results suggest a high inversion degree to an extent that the completely random configuration is achieved in MgAl2O4 induced by the high density electronic excitation under swift heavy ion irradiation.
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Affiliation(s)
- S Yoshioka
- Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka, 819-0395, Japan.
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24
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Gulshan MA, Rahman MM, Matsumura S, Higuchi T, Umezawa N, Ikawa Y. Biogenic triamine and tetraamine activate core catalytic ability of Tetrahymena group I ribozyme in the absence of its large activator module. Biochem Biophys Res Commun 2018; 496:594-600. [DOI: 10.1016/j.bbrc.2018.01.085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
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25
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Murakami T, Matsumura S. Reversible myelopathy with vitamin B12 deficiency after cerebral infarction-like lesions. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.3621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Oi H, Fujita D, Suzuki Y, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes. J Biochem 2017; 161:451-462. [PMID: 28096453 DOI: 10.1093/jb/mvw093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/15/2016] [Indexed: 11/12/2022] Open
Abstract
RNA is a biopolymer that is attractive for constructing nano-scale objects with complex structures. Three-dimensional (3D) structures of naturally occurring RNAs often have modular architectures. The 3D structure of a group I (GI) ribozyme from Tetrahymena has a typical modular architecture, which can be separated into two structural modules (ΔP5 and P5abc). The fully active ribozyme can be reconstructed by assembling the two separately prepared modules through highly specific and strong assembly between ΔP5 ribozyme and P5abc RNA. Such non-covalent assembly of the two modules allows the design of polygonal RNA nano-structures. Through rational redesign of the parent GI ribozyme, we constructed variant GI ribozymes as unit RNAs for polygonal-shaped (closed) oligomers with catalytic activity. Programmed trimerization and tetramerization of the unit RNAs afforded catalytically active nano-sized RNA triangles and squares, the structures of which were directly observed by atomic force microscopy (AFM).
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Affiliation(s)
- Hiroki Oi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Daisuke Fujita
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan
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27
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Matsumura S, Kun Á, Ryckelynck M, Coldren F, Szilágyi A, Jossinet F, Rick C, Nghe P, Szathmáry E, Griffiths AD. Transient compartmentalization of RNA replicators prevents extinction due to parasites. Science 2017; 354:1293-1296. [PMID: 27940874 DOI: 10.1126/science.aag1582] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/09/2016] [Indexed: 12/18/2022]
Abstract
The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin of life. However, parasitic replicators would take over and would have prevented life from taking off unless the replicators were compartmentalized in reproducing protocells. Paradoxically, control of protocell reproduction would seem to require evolved replicators. We show here that a simpler population structure, based on cycles of transient compartmentalization (TC) and mixing of RNA replicators, is sufficient to prevent takeover by parasitic mutants. TC tends to select for ensembles of replicators that replicate at a similar rate, including a diversity of parasites that could serve as a source of opportunistic functionality. Thus, TC in natural, abiological compartments could have allowed life to take hold.
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Affiliation(s)
- Shigeyoshi Matsumura
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 Rue Vauquelin, 75231 Paris Cedex 05, France.,Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France.,Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
| | - Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany.,MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
| | - Michael Ryckelynck
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France.,Architecture et Réactivité de l'ARN, CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Faith Coldren
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
| | - András Szilágyi
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany.,MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical Biology, Budapest, Hungary
| | - Fabrice Jossinet
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Christian Rick
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France.,Architecture et Réactivité de l'ARN, CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Philippe Nghe
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 Rue Vauquelin, 75231 Paris Cedex 05, France
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany. .,MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Budapest, Hungary.,Conflict and Cooperation in Evolutionary Systems Program, Institute of Advanced Studies, Kőszeg, Hungary
| | - Andrew D Griffiths
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 Rue Vauquelin, 75231 Paris Cedex 05, France. .,Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
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28
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Tanaka T, Hirata Y, Tominaga Y, Furuta H, Matsumura S, Ikawa Y. Heterodimerization of Group I Ribozymes Enabling Exon Recombination through Pairs of Cooperative trans-Splicing Reactions. Chembiochem 2017; 18:1659-1667. [PMID: 28556398 DOI: 10.1002/cbic.201700053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Indexed: 12/31/2022]
Abstract
Group I (GI) self-splicing ribozymes are attractive tools for biotechnology and synthetic biology. Several trans-splicing and related reactions based on GI ribozymes have been developed for the purpose of recombining their target mRNA sequences. By combining trans-splicing systems with rational modular engineering of GI ribozymes it was possible to achieve more complex editing of target RNA sequences. In this study we have developed a cooperative trans-splicing system through rational modular engineering with use of dimeric GI ribozymes derived from the Tetrahymena group I intron ribozyme. The resulting pairs of ribozymes exhibited catalytic activity depending on their selective dimerization. Rational modular redesign as performed in this study would facilitate the development of sophisticated regulation of double or multiple trans-splicing reactions in a cooperative manner.
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Affiliation(s)
- Takahiro Tanaka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yusuke Hirata
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
| | - Yuto Tominaga
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan
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29
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Matsumura S, Quispe-Salcedo A, Schiller CM, Shin JS, Locke BM, Yakar S, Shimizu E. IGF-1 Mediates EphrinB1 Activation in Regulating Tertiary Dentin Formation. J Dent Res 2017; 96:1153-1161. [PMID: 28489485 DOI: 10.1177/0022034517708572] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Eph receptors belong to a subfamily of receptor tyrosine kinases that are activated by membrane-spanning ligands called ephrins. Previously, we demonstrated that the ephrinB1-EphB2 interaction regulates odontogenic/osteogenic differentiation from dental pulp cells (DPCs) in vitro. The goal of this study was to identify the molecular mechanisms regulated by the EphB2/ephrinB1 system that govern tertiary dentin formation in vitro and in vivo. During tooth development, ephrinB1, and EphB2 were expressed in preodontoblast and odontoblasts at postnatal day 4. EphrinB1 was continuously expressed in odontoblasts and odontoblastic processes until the completion of tooth eruption. In addition, ephrinB1 was expressed in odontoblastic processes 2 wk following tooth injury without pulp exposure, whereas EphB2 was expressed in the center of pulp niches but not odontoblasts. In a model of tooth injury with pulp exposure, ephrinB1 was strongly expressed in odontoblasts 4 wk postinjury. In vitro studies with human and mouse DPCs treated with calcium hydroxide (CH) or mineral trioxide aggregate (MTA) showed an increased expression of insulin-like growth factor 1 (IGF-1). Experiments using several inhibitors of IGF-1 receptor signaling revealed that inhibiting the Ras/Raf-1/MAPK pathway inhibited EphB2 expression, and inhibiting the PI3K/Akt/mTOR pathway specifically inhibited ephrinB1 gene expression. Tooth injury in mice with odontoblast-specific IGF-1 receptor ablation exhibited a reduced tertiary dentin volume, mineral density, and ephrinB1 expression 4 wk following injury. We conclude that the IGF-1/ephrinB1 axis plays significant roles in the early stages of tooth injury. Further research is needed to fully understand the potential of targeting ephrinB1 as a regenerative pulp therapy.
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Affiliation(s)
- S Matsumura
- 1 Department of Oral and Maxillofacial Radiology, University of Connecticut Health Center, School of Dental Medicine, Farmington, Connecticut, USA
| | - A Quispe-Salcedo
- 2 Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, USA
| | - C M Schiller
- 2 Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, USA
| | - J S Shin
- 2 Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, USA
| | - B M Locke
- 2 Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, USA
| | - S Yakar
- 2 Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, USA
| | - E Shimizu
- 2 Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, USA.,3 Oral Biology Department, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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30
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Ojima T, Nakamori M, Nakamura M, Katsuda M, Hayata K, Matsumura S, Iwahashi M, Yamaue H. Phase I/II study of divided-dose docetaxel, cisplatin and fluorouracil for patients with recurrent or metastatic squamous cell carcinoma of the esophagus. Dis Esophagus 2017; 30:1-7. [PMID: 26725778 DOI: 10.1111/dote.12450] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Squamous cell carcinoma of the esophagus (SCCE) has a poor prognosis compared with other gastrointestinal cancers. Many patients present with locoregional unresectable or metastatic disease at the time of diagnosis. For these patients with metastatic esophageal cancer, chemotherapy is generally indicated. The aim of this phase I/II study was to evaluate the efficacy and safety of the combined use of docetaxel, cisplatin (CDDP) and 5-fluorouracil (5-FU)(DCF) in patients with recurrent/metastatic SCCE. This study adopted divided doses of docetaxel and CDDP in order to reduce the toxicities of the treatment. The dose of docetaxel was escalated using the following protocol in the phase I stage: level 1, 30 mg/m2; level 2, 35 mg/m2 and level 3, 40 mg/m2, which was intravenously infused for 2 hours on days 1 and 8. CDDP was administered at a dose of 12 mg/m2 infused for 4 hours on days 1-5. The 5-FU was administered at a dose of 600 mg/m2 continuously infused from day 1 to 5. This regimen was repeated every 4 weeks. The study subjects were nine patients (phase I) and 48 patients (phase II). The recommended dose was determined as level 3 in phase I. In the phase II stage, the overall response rate was 62.5%, with a complete response rate of 12.5%. The median progression-free survival was 6 months, and the median overall survival was 13 months. Grade 3/4 toxicities of leukopenia, neutropenia and febrile neutropenia occurred in 64.6%, 68.8% and 14.6% of the patients, while grade 3/4 non-hematological toxicities were relatively rare. No treatment-related death was recorded. This modified DCF regimen with divided doses can be a tolerable and useful regimen of definitive chemotherapy for unresectable SCCE because of its high efficacy, although adequate care for severe neutropenia must be administered.
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Affiliation(s)
- T Ojima
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - M Nakamori
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - M Nakamura
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - M Katsuda
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - K Hayata
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - S Matsumura
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - M Iwahashi
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
| | - H Yamaue
- Second Department of Surgery, Wakayama Medical University, School of Medicine, Wakayama, Japan
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31
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Abstract
We designed and constructed a dimer of the Tetrahymena group I ribozyme the activity of which is regulated by self-dimerization. This dimer was rationally designed by utilizing the P5abc and ΔP5abc domains as large RNA motifs. This strategy enabled us to install large ribozyme functions into an RNA structure. This is a step toward expanding the field of RNA nanotechnology beyond the limitation of using only relatively small functional motifs. Self-dimerization can also be rationally programmed by modular engineering of RNA interaction motifs. In this chapter, we present the procedure for the rational design and construction of large ribozyme domains based on RNA tertiary structures. We also describe the electrophoresis mobility shift assay (EMS) and several ribozyme activity assays to confirm the ribozyme function and its regulation. We have succeeded in construction of tecto-GIRz.
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Affiliation(s)
- Takahiro Tanaka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshiya Ikawa
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan.
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Takaki S, Yasuda K, Yamamoto T, Matsumura S, Ishikawa N. Structure of ion tracks in ceria irradiated with high energy xenon ions. Progress in Nuclear Energy 2016. [DOI: 10.1016/j.pnucene.2016.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Tanaka T, Matsumura S, Furuta H, Ikawa Y. Tecto-GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self-Dimerization. Chembiochem 2016; 17:1448-55. [DOI: 10.1002/cbic.201600190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Takahiro Tanaka
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry; Graduate School of Science and Engineering; University of Toyama; Gofuku 3190 Toyama 930-8555 Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
| | - Yoshiya Ikawa
- Department of Chemistry; Graduate School of Science and Engineering; University of Toyama; Gofuku 3190 Toyama 930-8555 Japan
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Inuzuka S, Nishimura KI, Kakizawa H, Fujita Y, Furuta H, Matsumura S, Ikawa Y. Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism. J Biochem 2016; 160:153-62. [PMID: 27033943 DOI: 10.1093/jb/mvw026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/21/2016] [Indexed: 12/23/2022] Open
Abstract
The Vc2 riboswitch possesses an aptamer domain belonging to the class-I c-di-GMP riboswitch family. This domain has been analysed and the molecular mechanism by which it recognizes the c-di-GMP ligand has been elucidated. On the other hand, the regulatory mechanism of the full-length Vc2 riboswitch to control its downstream open reading frame (ORF) remains largely unknown. In this study, we performed in vivo reporter assays and in vitro biochemical analyses of the full-length riboswitch and its aptamer domain. We evaluated the results of in vivo and in vitro analyses to elucidate the regulatory mechanism of the Vc2 riboswitch. The present results suggest that recognition of c-di-GMP ligand by the Vc2 riboswitch aptamer domain downregulates expression of its downstream ORF primarily at the translational level.
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Affiliation(s)
- Saki Inuzuka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Kei-Ichiro Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hitoshi Kakizawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yuki Fujita
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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Abstract
Tertiary interactions between a new RNA motif and RNA tetraloops were analyzed to determine whether this new motif shows preference for a GCGA tetraloop. In the structural context of a ligase ribozyme, this motif discriminated GCGA loop from 3 other tetraloops. The affinity between the GCGA loop and its receptor is strong enough to carry out the ribozyme activity.
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Affiliation(s)
- Airi Furukawa
- a Department of Chemistry , Graduate School of Science and Engineering, University of Toyama , Toyama , Japan
| | - Takaya Maejima
- a Department of Chemistry , Graduate School of Science and Engineering, University of Toyama , Toyama , Japan
| | - Shigeyoshi Matsumura
- a Department of Chemistry , Graduate School of Science and Engineering, University of Toyama , Toyama , Japan
| | - Yoshiya Ikawa
- a Department of Chemistry , Graduate School of Science and Engineering, University of Toyama , Toyama , Japan
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Inuzuka S, Matsumura S, Ikawa Y. Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules. J Biosci Bioeng 2016; 122:183-7. [PMID: 26968125 DOI: 10.1016/j.jbiosc.2016.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 01/31/2023]
Abstract
Cyclic diguanylate (c-di-GMP) is a second messenger of bacteria and its detection is an important issue in basic and applied microbiology. As c-di-GMP riboswitch ligand-binding domains (aptamer domains) capture c-di-GMP with high affinity and selectivity, they are promising platforms for the development of RNA-based c-di-GMP sensors. We analyzed two previously reported c-di-GMP sensor RNAs derived from the Vc2 riboswitch. We also designed and tested their variants, some of which showed improved properties as RNA-based c-di-GMP sensors.
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Affiliation(s)
- Saki Inuzuka
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
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Uno K, Nishizawa D, Seo S, Takayama K, Matsumura S, Sakai N, Ohi K, Nabeshima T, Hashimoto R, Ozaki N, Hasegawa J, Sato N, Tanioka F, Sugimura H, Fukuda KI, Higuchi S, Ujike H, Inada T, Iwata N, Sora I, Iyo M, Kondo N, Won MJ, Naruse N, Uehara-Aoyama K, Itokawa M, Yamada M, Ikeda K, Miyamoto Y, Nitta A. The Piccolo Intronic Single Nucleotide Polymorphism rs13438494 Regulates Dopamine and Serotonin Uptake and Shows Associations with Dependence-Like Behavior in Genomic Association Study. Curr Mol Med 2016; 15:265-74. [PMID: 25817861 DOI: 10.2174/1566524015666150330145722] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 02/27/2015] [Accepted: 03/24/2015] [Indexed: 11/22/2022]
Abstract
Piccolo (PCLO) inhibits methamphetamine-induced neuropharmacological effects via modulation of dopamine (DA) uptake and regulation of the transport of synaptic vesicles in neuronal cells. Clinical studies have recently suggested that the single nucleotide polymorphism (SNP) rs13438494 in the intron 24 of the PCLO gene is associated with psychiatric disorder, in the meta-analysis of GWAS. Therefore, in this study, we attempted to evaluate the possible role of the PCLO SNP in the mechanisms of uptake of monoamines. To characterize rs13438494 in the PCLO gene, we constructed plasmids carrying either the C or A allele of the SNP and transiently transfected them into SH-SY5Y cells to analyze genetic effects on the splicing of PCLO mRNA. The C and A allele constructs produced different composition of the transcripts, indicating that the intronic SNP does affect the splicing pattern. We also transfected DA and serotonin (5-hydroxytryptamine; 5- HT) transporters into cells and analyzed their uptakes to elucidate the association to psychiatric disorders. In the cells transfected with the C allele, both the DA and 5-HT uptake were enhanced compared to the A allele. We also conducted a clinical study, in order to clarify the genetic associations. PCLO rs13438494 exhibits a relationship with the symptoms of drug dependence or related parameters, such as the age of first exposure to methamphetamine, eating disorders, tobacco dependence and fentanyl requirement. Our findings suggest that rs13438494 is associated with drug abuse and contributes to the pathogenesis of psychiatric disorders via modulation of neurotransmitter turnover.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - A Nitta
- Department of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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Matsumura S, Ikawa Y. Artificial ligase ribozymes isolated by a "design and selection" strategy. Methods Mol Biol 2015; 1316:113-25. [PMID: 25967057 DOI: 10.1007/978-1-4939-2730-2_10] [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: 02/18/2023]
Abstract
We developed a new in vitro selection strategy "design and selection" to isolate effectively artificial ribozymes (catalytic RNAs). An overall RNA structure (scaffold) is initially designed, and then a relatively short randomized sequence is installed at the reaction point of the scaffold, followed by the in vitro selection. This method can reduce the length of randomized sequence, providing large coverage of the sequence space in contrast with the conventional way, which makes the selection experiment effectively. Additionally, further analysis of ribozymes obtained by this approach is practically easy since the overall molecular structure is predesigned and well known. Here we show the procedure to isolate artificial RNA ligase ribozymes by this strategy. We have succeeded in isolation of the designed and selected ligase (DSL) ribozymes.
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Affiliation(s)
- Shigeyoshi Matsumura
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama Prefecture, 930-0087, Japan,
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Matsumura S, Ito T, Tanaka T, Furuta H, Ikawa Y. Modulation of group I ribozyme activity by cationic porphyrins. Biology (Basel) 2015; 4:251-63. [PMID: 25811638 PMCID: PMC4498298 DOI: 10.3390/biology4020251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/03/2015] [Indexed: 11/16/2022]
Abstract
The effects of cationic porphyrins on the catalytic activities of four group I ribozymes were investigated. A cationic porphyrin possessing four pyridinium moieties (pPyP) inhibited two group IC3 ribozymes (Syn Rz and Azo Rz) and a group IC1 ribozyme (Tet Rz). In the case of a group IA2 ribozyme (Td Rz), however, pPyP served not only as an inhibitor but also as an activator, and the effects of pPyP were dependent on its concentration. To analyze the structural and electronic factors determining the effects of pPyP on group I ribozymes, three cationic porphyrins (pPyNCP, pPyF4P, and TMPyP) were also examined. As interactions between small organic molecules and nucleic acids are attractive and important issues in biochemistry and biotechnology, this study contributes to the development of porphyrin-based molecules that can modulate functions of structured RNA molecules.
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Affiliation(s)
- Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
| | - Tatsunobu Ito
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Takahiro Tanaka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
- Center for Molecular Systems, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
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Matsumura S, Higa K, Igarashi T, Takaichi S, Tonogi M, Shinozaki N, Shimazaki J, Yamane GY. Characterization of mesenchymal progenitor cell populations from non-epithelial oral mucosa. Oral Dis 2014; 21:361-72. [PMID: 25180458 DOI: 10.1111/odi.12288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 04/06/2012] [Revised: 12/27/2013] [Accepted: 08/26/2014] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The characteristics of cell populations extracted from oral mucosal non-epithelial tissues and their ability to differentiate were evaluated in vitro as a potential source of cells for mandibular and corneal regeneration. MATERIALS AND METHODS Oral mucosal non-epithelial cells (OMNECs) were extracted from tissue samples and were studied by flow cytometry and RT-PCR. Cells differentiating into osteoblasts, adipocytes, chondrocytes, neurocytes, or keratocytes were characterized by RT-PCR and cell staining. RESULTS OMNECs expressed CD44, CD90, CD105, CD166, and STRO-1 antigens, which are markers for mesenchymal stem cells. In addition, Oct3/4, c-Myc, Nanog, KLF4, and Rex, which are expressed by embryonic or pluripotent stem cells, were detected by RT-PCR. Expression of CD49d, CD56, and PDGFRα, proteins closely associated with the neural crest, was observed in OMNECs, as was expression of Twist1, Sox9, Snail1 and Snail2, which are early neural crest and neural markers. Specific differentiation markers were expressed in OMNECs after differentiation into osteoblasts, adipocytes, chondrocytes, or keratocytes. CONCLUSIONS Populations of OMNECs may contain both mesenchymal stem cells and neural crest origin cells and are a potential cell source for autologous regeneration of mandibular or corneal stroma.
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Affiliation(s)
- S Matsumura
- Department of Oral Medicine, Oral and Maxillofacial Surgery, Tokyo Dental College, Chiba, Japan
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Ochiai T, Shioya A, Honma H, Saitoh Y, Matsumura S, Ban D, Irie T, Kudo A, Nakamura N, Fujikawa T, Itai A, Tanaka S, Arii S, Yamaoka S, Tanabe M. Combination Treatment of IκB Kinase β Inhibitor IMD-0354 and Gemcitabine Suppresses Oncogenic Proliferation of Pancreatic Cancer Cells. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Timpel M, Wanderka N, Schlesiger R, Yamamoto T, Isheim D, Schmitz G, Matsumura S, Banhart J. Sr-Al-Si co-segregated regions in eutectic Si phase of Sr-modified Al-10Si alloy. Ultramicroscopy 2013; 132:216-21. [PMID: 23298536 DOI: 10.1016/j.ultramic.2012.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 09/30/2012] [Accepted: 10/20/2012] [Indexed: 11/16/2022]
Abstract
The addition of 200 ppm strontium to an Al-10 wt% Si casting alloy changes the morphology of the eutectic silicon phase from coarse plate-like to fine fibrous networks. In order to clarify this modification mechanism the location of Sr within the eutectic Si phase has been investigated by a combination of high-resolution methods. Whereas three-dimensional atom probe tomography allows us to visualise the distribution of Sr on the atomic scale and to analyse its local enrichment, transmission electron microscopy yields information about the crystallographic nature of segregated regions. Segregations with two kinds of morphologies were found at the intersections of Si twin lamellae: Sr-Al-Si co-segregations of rod-like morphology and Al-rich regions of spherical morphology. Both are responsible for the formation of a high density of multiple twins and promote the anisotropic growth of the eutectic Si phase in specific crystallographic directions during solidification. The experimental findings are related to the previously postulated mechanism of "impurity induced twinning".
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Affiliation(s)
- M Timpel
- Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin, Germany.
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Fukushima K, Tsukimori K, Li D, Takao T, Morokuma S, Kato K, Seki H, Takeda S, Matsumura S, Wake N. Effect of transient TCDD exposure on immortalized human trophoblast-derived cell lines. Hum Exp Toxicol 2011; 31:550-6. [PMID: 22027506 DOI: 10.1177/0960327111424305] [Citation(s) in RCA: 4] [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] [Indexed: 12/29/2022]
Abstract
Low level, antenatal exposure to dioxins is associated with low birth weight, which in turn is associated with long-term sequelae. We exposed the human extravillous cytotrophoblast (EVT) lines HTR-8/SV40 and TCL1 to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and assessed cell growth, invasion, and differentiation. TCDD had no effect on cell proliferation, invasion, or tube formation in Matrigel. The EVT-derived cells expressed a functional aryl hydrocarbon receptor protein; however, TCDD exposure did not alter expression levels of proteins involved in EVT differentiation in early pregnancy, including hypoxia-inducible factor 1A (HIF1A), vascular endothelial growth factor (VEGF), Integrin A1, A6, and AVB3. These results suggest that the reduction in fetal weight induced by dioxin is not the result of vascular remodeling via EVT dysfunction.
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Affiliation(s)
- K Fukushima
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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Matsumura S, Sakurai K, Shinomiya T, Fujitani N, Key K, Ohashi M. Biochemical and immunohistochemical characterization of the isoforms of myosin and actin in human placenta. Placenta 2011; 32:347-55. [PMID: 21420731 DOI: 10.1016/j.placenta.2011.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/24/2011] [Accepted: 02/24/2011] [Indexed: 11/29/2022]
Abstract
Human placenta has long been known to contain large quantities of smooth muscle-type myosin and actin, while precise isoform compositions of its contractile proteins are not known. To determine the isoform compositions, myosin and actin were extracted from human term placentas and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting by using isoform-specific monoclonal anti-myosin and anti-actin antibodies. The placental myosin was found to be composed of about 65% of a nonmuscle-type heavy chain isoform (MIIA), each about 15% of two smooth muscle-type heavy chain isoforms (SM1 and SM2) and about 5% of a brain/fetus-type heavy chain isoform (MIIB2). Whereas the MIIA isoform was present in both vascular and extravascular tissues, the SM1 isoform was localized almost only in the vascular tissue. Similarly, human term placenta was found to contain approximately 60, 30, and 10% of β-nonmuscle, α-smooth muscle, γ-smooth muscle actin isoforms, respectively. The β-nonmuscle actin was located primarily in the extravascular tissue, while the α-smooth muscle actin was located mostly in the vascular tissue. The extravascular tissue of the human term placenta thus appears to be composed of almost only nonmuscle-type isoforms of contractile proteins. The vascular tissue appears to be composed of both smooth muscle-type and nonmuscle-type isoforms of contractile proteins.
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Affiliation(s)
- S Matsumura
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Suma, Japan.
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Matsumura S, Soeda T, Zaluzec NJ, Kinoshita C. Electron Channeling X-ray Microanalysis for Cation Configuration in Irradiated Magnesium Aluminate Spinel. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-589-129] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractHigh angular resolution electron channeling x-ray spectroscopy (HARECXS) was examined as a practical tool to locate lattice-ions in spinel crystals. The orientation dependent intensity distribution of emitted x-rays obtained by HARECXS is so sensitive to lattice-ion configuration in the illuminated areas that the occupation probabilities on specific positions in the crystal lattice can be determined accurately through comparison with the theoretical rocking curves. HARECXS measurements have revealed partially disordered cation arrangement in MgO·nAl2O3 with n= 1.0 and 2.4. Most A13+ lattice-ions occupy the octahedral (VI) sites with 6-fold coordination, while Mg2+ lattice-ions reside on both the tetrahedral (IV) and the octahedral (VI) sites. The structural vacancies are enriched in the IV-sites. Further evacuation of cations from the IV-sites to the VI-sites is recognized in a disordering process induced by irradiation with 1 MeV Ne+ ions up to 8.9 dpa at 870 K.
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Matsumura S, Takagi K, Okuda-Ashitaka E, Lu J, Naritsuka H, Yamaguchi M, Ito S. Characterization of nestin expression in the spinal cord of GFP transgenic mice after peripheral nerve injury. Neuroscience 2010; 170:942-53. [PMID: 20673789 DOI: 10.1016/j.neuroscience.2010.07.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 07/15/2010] [Accepted: 07/15/2010] [Indexed: 12/14/2022]
Abstract
Many studies have shown that activation and increase in the number of astrocytes and microglia in the spinal cord participate in the initiation and maintenance of neuropathic pain, but little attention has been paid to the responses of neural progenitor cells to peripheral nerve injury. Nestin, a class VI intermediate filament protein, is expressed both in neuronal and glial progenitors as well as in their common precursors; and nestin-positive cells appear in the brain and spinal cord following various forms of damage to these regions. To clarify the responses of neural progenitor cells to nerve injury, we applied L5 spinal nerve transection (L5-SNT) to nestin-promoter GFP (pNestin-GFP) transgenic mice to narrow the target to them. While pNestin-GFP expression was strongly retained in the ependyma lining the central canal of the transgenic spinal cord even in adulthood, it was markedly reduced in the dorsal horn during postnatal development by day 7. Increases in pNestin-GFP expression and labeling by the proliferation marker 5-bromodeoxyuridine were broadly found in the dorsal horn of adult mice on day 3 after L5-SNT. On the other hand, the activation and increase in number of microglia and astrocytes are restricted to the superficial layer of the dorsal horn, the central terminal of injured primary afferent fibers. Purinergic P2X agonist α, β-MeATP increased [Ca(2+)]i in nestin-positive cells in the superficial layer ipsilateral to nerve injury and P2 receptor antagonists suramin and pyridoxalphosphate-6-azophenyl-2,4-disulphonic acid (PPADS) blocked the expression and elongation of pNestin-GFP fibers in the slice culture of the spinal cord. These results with pNestin-GFP transgenic mice demonstrate that nestin-positive cells proliferate in the dorsal horn in response to peripheral nerve injury and suggest that ATP may contribute to the expression of nestin and activation of neural progenitor cells after nerve injury.
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Affiliation(s)
- S Matsumura
- Department of Medical Chemistry, Kansai Medical University, Moriguchi, Osaka 570-8506, Japan
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Ishikawa J, Matsumura S, Jaeger L, Inoue T, Furuta H, Ikawa Y. Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules. Arch Biochem Biophys 2009; 490:163-70. [PMID: 19728985 PMCID: PMC2826975 DOI: 10.1016/j.abb.2009.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [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: 07/21/2009] [Revised: 08/26/2009] [Accepted: 08/26/2009] [Indexed: 12/28/2022]
Abstract
The DSL ribozyme is a class of artificial ligase ribozymes with a highly modular architecture, which catalyzes template-directed RNA ligation on a helical substrate module that can be either covalently connected (cis-DSL) or physically separated (trans-DSL) from the catalytic module. Substrate recognition by the catalytic module is promoted by one or two sets of GNRA/receptor interactions acting as clamps in the cis or trans configurations, respectively. In this study, we have rationally designed and analyzed the catalytic and self-assembly properties of several trans-DSL ribozymes with different sets of natural and artificial GNRA-receptor clamps. Two variants newly designed in this study showed significantly enhanced catalytic properties with respect of the original trans-DSL construct. While this work allows dissection of the turnover and catalytic properties of the trans-DSL ribozyme, it also emphasizes the remarkable modularity of RNA tertiary structure for nano-construction of complex functions.
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Affiliation(s)
- Junya Ishikawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Shigeyoshi Matsumura
- Institut de Science et d'Ingenierie Supramoleculaires (ISIS), Université Louis Pasteur, 8 Allée Gaspard Monge, B. P. 70028, 67083 Strasbourg Cedex, France
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California at Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Tan Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- ICORP, Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshiya Ikawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- PRESTO, Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
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Bramanti B, Thomas MG, Haak W, Unterlaender M, Jores P, Tambets K, Antanaitis-Jacobs I, Haidle MN, Jankauskas R, Kind CJ, Lueth F, Terberger T, Hiller J, Matsumura S, Forster P, Burger J. Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 2009; 326:137-40. [PMID: 19729620 DOI: 10.1126/science.1176869] [Citation(s) in RCA: 372] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
After the domestication of animals and crops in the Near East some 11,000 years ago, farming had reached much of central Europe by 7500 years before the present. The extent to which these early European farmers were immigrants or descendants of resident hunter-gatherers who had adopted farming has been widely debated. We compared new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into central Europe at the onset of the Neolithic.
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Affiliation(s)
- B Bramanti
- Institute for Anthropology, University of Mainz, Mainz, Germany.
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Matsumura S, Ohmori R, Saito H, Ikawa Y, Inoue T. Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction. FEBS Lett 2009; 583:2819-26. [PMID: 19631647 DOI: 10.1016/j.febslet.2009.07.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/15/2009] [Accepted: 07/18/2009] [Indexed: 11/24/2022]
Abstract
We previously developed a synthetic cis-acting RNA ligase ribozyme with 3'-5' joining activity termed "DSL" (designed and selected ligase). DSL was easily transformed into a trans-acting form because of its highly modular architecture. In this study, we investigated the modular properties and turnover capabilities of a trans-acting DSL, tDSL-1/GUAA. tDSL-1/GUAA exhibited remarkably high activity compared with the parental cis-acting DSL, and it attained a high turnover number. Taken together, the results indicate that a loop-receptor interaction plays a significant role in determining the activity of the trans-acting ribozyme and in its ability to perform multiple turnovers of the reaction.
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Oguma R, Matsumura S, Eguchi T. Kinetics of B2- and D0(3)-type ordering and formation of domain structures in Fe-Al alloys. J Phys Condens Matter 2008; 20:275225. [PMID: 21694386 DOI: 10.1088/0953-8984/20/27/275225] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Time-dependent Ginzburg-Landau (TDGL) formulation has been developed for the ordering processes of B2 and D0(3) types in binary alloy systems. In the formulation, three order parameters are defined in order to describe the state of order. Equivalent variants of B2 and D0(3) structures are distinguished using these order parameters. The mean-field free energy is defined in the form of a Landau-type expansion using the order parameters and a composition parameter. Interface energies due to local variations in the degrees of order and concentration are given with a gradient square approximation. Kinetic equations are derived from the Ginzburg-Landau-type potential in order to describe the time-evolutions of the order parameters and the concentration. Numerical simulations of the kinetic equations have been performed for B2- and D0(3)-type ordering as well as concurrent ordering and phase separation to disordered A2+D0(3). The simulated results provide a good reproduction of the formation processes of B2 and D0(3) ordered domains in an Fe(3)Al alloy.
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Affiliation(s)
- R Oguma
- Department of Applied Physics, Fukuoka University, Nanakuma 8-19-1, Jonanku, Fukuoka 814-0180, Japan
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