Cargando…
Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling
BACKGROUD: Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active met...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890716/ https://www.ncbi.nlm.nih.gov/pubmed/24308360 http://dx.doi.org/10.1186/1471-2164-14-857 |
_version_ | 1782299305310158848 |
---|---|
author | Chen, Junfeng Dong, Xin Li, Qing Zhou, Xun Gao, Shouhong Chen, Ruibing Sun, Lianna Zhang, Lei Chen, Wansheng |
author_facet | Chen, Junfeng Dong, Xin Li, Qing Zhou, Xun Gao, Shouhong Chen, Ruibing Sun, Lianna Zhang, Lei Chen, Wansheng |
author_sort | Chen, Junfeng |
collection | PubMed |
description | BACKGROUD: Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset of I. indigotica. RESULTS: A database of 36,367 unigenes (average length = 1,115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, 104 unigenes were identified covering most of the catalytic steps in the general biosynthetic pathways of indole, terpenoid, and phenylpropanoid. Subsequently, the organ-specific expression patterns of the genes involved in these pathways, and their responses to methyl jasmonate (MeJA) induction, were investigated. Metabolites profile of effective phenylpropanoid showed accumulation pattern of secondary metabolites were mostly correlated with the transcription of their biosynthetic genes. According to the analysis of UDP-dependent glycosyltransferases (UGT) family, several flavonoids were indicated to exist in I. indigotica and further identified by metabolic profile using UPLC/Q-TOF. Moreover, applying transcriptome co-expression analysis, nine new, putative UGTs were suggested as flavonol glycosyltransferases and lignan glycosyltransferases. CONCLUSIONS: This database provides a pool of candidate genes involved in biosynthesis of effective metabolites in I. indigotica. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb. |
format | Online Article Text |
id | pubmed-3890716 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-38907162014-01-15 Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling Chen, Junfeng Dong, Xin Li, Qing Zhou, Xun Gao, Shouhong Chen, Ruibing Sun, Lianna Zhang, Lei Chen, Wansheng BMC Genomics Research Article BACKGROUD: Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset of I. indigotica. RESULTS: A database of 36,367 unigenes (average length = 1,115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, 104 unigenes were identified covering most of the catalytic steps in the general biosynthetic pathways of indole, terpenoid, and phenylpropanoid. Subsequently, the organ-specific expression patterns of the genes involved in these pathways, and their responses to methyl jasmonate (MeJA) induction, were investigated. Metabolites profile of effective phenylpropanoid showed accumulation pattern of secondary metabolites were mostly correlated with the transcription of their biosynthetic genes. According to the analysis of UDP-dependent glycosyltransferases (UGT) family, several flavonoids were indicated to exist in I. indigotica and further identified by metabolic profile using UPLC/Q-TOF. Moreover, applying transcriptome co-expression analysis, nine new, putative UGTs were suggested as flavonol glycosyltransferases and lignan glycosyltransferases. CONCLUSIONS: This database provides a pool of candidate genes involved in biosynthesis of effective metabolites in I. indigotica. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb. BioMed Central 2013-12-05 /pmc/articles/PMC3890716/ /pubmed/24308360 http://dx.doi.org/10.1186/1471-2164-14-857 Text en Copyright © 2013 Chen et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Chen, Junfeng Dong, Xin Li, Qing Zhou, Xun Gao, Shouhong Chen, Ruibing Sun, Lianna Zhang, Lei Chen, Wansheng Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling |
title | Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling |
title_full | Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling |
title_fullStr | Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling |
title_full_unstemmed | Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling |
title_short | Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling |
title_sort | biosynthesis of the active compounds of isatis indigotica based on transcriptome sequencing and metabolites profiling |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890716/ https://www.ncbi.nlm.nih.gov/pubmed/24308360 http://dx.doi.org/10.1186/1471-2164-14-857 |
work_keys_str_mv | AT chenjunfeng biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT dongxin biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT liqing biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT zhouxun biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT gaoshouhong biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT chenruibing biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT sunlianna biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT zhanglei biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling AT chenwansheng biosynthesisoftheactivecompoundsofisatisindigoticabasedontranscriptomesequencingandmetabolitesprofiling |