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Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus

Mallotus japonicus 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 est...

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Autores principales: Rai, Megha, Rai, Amit, Mori, Tetsuya, Nakabayashi, Ryo, Yamamoto, Manami, Nakamura, Michimi, Suzuki, Hideyuki, Saito, Kazuki, Yamazaki, Mami
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396295/
https://www.ncbi.nlm.nih.gov/pubmed/34445541
http://dx.doi.org/10.3390/ijms22168835
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author Rai, Megha
Rai, Amit
Mori, Tetsuya
Nakabayashi, Ryo
Yamamoto, Manami
Nakamura, Michimi
Suzuki, Hideyuki
Saito, Kazuki
Yamazaki, Mami
author_facet Rai, Megha
Rai, Amit
Mori, Tetsuya
Nakabayashi, Ryo
Yamamoto, Manami
Nakamura, Michimi
Suzuki, Hideyuki
Saito, Kazuki
Yamazaki, Mami
author_sort Rai, Megha
collection PubMed
description Mallotus japonicus 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 M. japonicus 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 M. japonicus represented by 2129 metabolite features. M. japonicus 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 M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. 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 M. japonicus.
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spelling pubmed-83962952021-08-28 Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus Rai, Megha Rai, Amit Mori, Tetsuya Nakabayashi, Ryo Yamamoto, Manami Nakamura, Michimi Suzuki, Hideyuki Saito, Kazuki Yamazaki, Mami Int J Mol Sci Article Mallotus japonicus 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 M. japonicus 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 M. japonicus represented by 2129 metabolite features. M. japonicus 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 M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. 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 M. japonicus. MDPI 2021-08-17 /pmc/articles/PMC8396295/ /pubmed/34445541 http://dx.doi.org/10.3390/ijms22168835 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Rai, Megha
Rai, Amit
Mori, Tetsuya
Nakabayashi, Ryo
Yamamoto, Manami
Nakamura, Michimi
Suzuki, Hideyuki
Saito, Kazuki
Yamazaki, Mami
Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus
title Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus
title_full Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus
title_fullStr Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus
title_full_unstemmed Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus
title_short Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus
title_sort gene-metabolite network analysis revealed tissue-specific accumulation of therapeutic metabolites in mallotus japonicus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396295/
https://www.ncbi.nlm.nih.gov/pubmed/34445541
http://dx.doi.org/10.3390/ijms22168835
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