Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit
The class I ligase ribozyme consists of 121 nucleotides and shows a high catalytic rate comparable to that found in natural proteinaceous polymerases. In this study, we aimed to identify the smaller active unit of the class I ligase ribozyme comprising ~50 nucleotides, comparable to the estimated le...
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| Format: | Article |
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MDPI AG
2023-07-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/12/7/1012 |
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| author | Miho Kasuga Hiromi Mutsuro-Aoki Tadashi Ando Koji Tamura |
| author_facet | Miho Kasuga Hiromi Mutsuro-Aoki Tadashi Ando Koji Tamura |
| author_sort | Miho Kasuga |
| collection | DOAJ |
| description | The class I ligase ribozyme consists of 121 nucleotides and shows a high catalytic rate comparable to that found in natural proteinaceous polymerases. In this study, we aimed to identify the smaller active unit of the class I ligase ribozyme comprising ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Based on the three-dimensional structure of the class I ligase ribozyme, mutants were prepared and their ligation activities were analyzed. Sufficient ligation activity was maintained even when shortening to 94 nucleotides. However, because it would be difficult to approach the target of ~50 nucleotides by removing only the partial structure, the class I ligase ribozyme was then split into two molecules. The ligation activity was maintained even when splitting into two molecules of 55 and 39 nucleotides. Using a system with similar split ribozymes, we analyzed the ligation activity of mutants C30, C47, and A71, which have been previously identified as the positions that contribute to catalytic activity, and discussed the structural basis of the activity of these bases. Our findings suggest the rationale for the class I ligase ribozyme’s assembling from multiple fragments that would be achievable with prebiotic synthesis. |
| first_indexed | 2024-03-11T01:17:18Z |
| format | Article |
| id | doaj.art-1fd2adbe3f76462aa965b9bcb4572666 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-11T01:17:18Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-1fd2adbe3f76462aa965b9bcb45726662023-11-18T18:24:21ZengMDPI AGBiology2079-77372023-07-01127101210.3390/biology12071012Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating UnitMiho Kasuga0Hiromi Mutsuro-Aoki1Tadashi Ando2Koji Tamura3Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanDepartment of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, JapanThe class I ligase ribozyme consists of 121 nucleotides and shows a high catalytic rate comparable to that found in natural proteinaceous polymerases. In this study, we aimed to identify the smaller active unit of the class I ligase ribozyme comprising ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Based on the three-dimensional structure of the class I ligase ribozyme, mutants were prepared and their ligation activities were analyzed. Sufficient ligation activity was maintained even when shortening to 94 nucleotides. However, because it would be difficult to approach the target of ~50 nucleotides by removing only the partial structure, the class I ligase ribozyme was then split into two molecules. The ligation activity was maintained even when splitting into two molecules of 55 and 39 nucleotides. Using a system with similar split ribozymes, we analyzed the ligation activity of mutants C30, C47, and A71, which have been previously identified as the positions that contribute to catalytic activity, and discussed the structural basis of the activity of these bases. Our findings suggest the rationale for the class I ligase ribozyme’s assembling from multiple fragments that would be achievable with prebiotic synthesis.https://www.mdpi.com/2079-7737/12/7/1012class I ligase ribozymeminimizationRNARNA worldorigin of life |
| spellingShingle | Miho Kasuga Hiromi Mutsuro-Aoki Tadashi Ando Koji Tamura Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit Biology class I ligase ribozyme minimization RNA RNA world origin of life |
| title | Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit |
| title_full | Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit |
| title_fullStr | Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit |
| title_full_unstemmed | Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit |
| title_short | Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit |
| title_sort | molecular anatomy of the class i ligase ribozyme for elucidation of the activity generating unit |
| topic | class I ligase ribozyme minimization RNA RNA world origin of life |
| url | https://www.mdpi.com/2079-7737/12/7/1012 |
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