Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i>
<i>Mallotus japonicus</i> is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In...
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MDPI AG
2021-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/16/8835 |
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| author | Megha Rai Amit Rai Tetsuya Mori Ryo Nakabayashi Manami Yamamoto Michimi Nakamura Hideyuki Suzuki Kazuki Saito Mami Yamazaki |
| author_facet | Megha Rai Amit Rai Tetsuya Mori Ryo Nakabayashi Manami Yamamoto Michimi Nakamura Hideyuki Suzuki Kazuki Saito Mami Yamazaki |
| author_sort | Megha Rai |
| collection | DOAJ |
| description | <i>Mallotus japonicus</i> is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for <i>M. japonicus</i> to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of <i>M. japonicus</i> represented by 2129 metabolite features. <i>M. japonicus</i> de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in <i>M. japonicus</i>. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of <i>M. japonicus</i>. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in <i>M. japonicus</i>. |
| first_indexed | 2024-03-10T08:45:01Z |
| format | Article |
| id | doaj.art-a718b8749a0547b3868f481dc3568d0a |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T08:45:01Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-a718b8749a0547b3868f481dc3568d0a2023-11-22T08:01:19ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-08-012216883510.3390/ijms22168835Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i>Megha Rai0Amit Rai1Tetsuya Mori2Ryo Nakabayashi3Manami Yamamoto4Michimi Nakamura5Hideyuki Suzuki6Kazuki Saito7Mami Yamazaki8Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanRIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, JapanRIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanDepartment of Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan<i>Mallotus japonicus</i> is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for <i>M. japonicus</i> to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of <i>M. japonicus</i> represented by 2129 metabolite features. <i>M. japonicus</i> de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in <i>M. japonicus</i>. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of <i>M. japonicus</i>. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in <i>M. japonicus</i>.https://www.mdpi.com/1422-0067/22/16/8835<i>Mallotus japonicus</i>medicinal plantsbiosynthesis of specialized metabolitesbergeninrutinWCNA |
| spellingShingle | Megha Rai Amit Rai Tetsuya Mori Ryo Nakabayashi Manami Yamamoto Michimi Nakamura Hideyuki Suzuki Kazuki Saito Mami Yamazaki Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i> International Journal of Molecular Sciences <i>Mallotus japonicus</i> medicinal plants biosynthesis of specialized metabolites bergenin rutin WCNA |
| title | Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i> |
| title_full | Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i> |
| title_fullStr | Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i> |
| title_full_unstemmed | Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i> |
| title_short | Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in <i>Mallotus japonicus</i> |
| title_sort | gene metabolite network analysis revealed tissue specific accumulation of therapeutic metabolites in i mallotus japonicus i |
| topic | <i>Mallotus japonicus</i> medicinal plants biosynthesis of specialized metabolites bergenin rutin WCNA |
| url | https://www.mdpi.com/1422-0067/22/16/8835 |
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