Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in rotenoid biosynthesis in the medicinal plant Mirabilis himalaica

Abstract

Mirabilis himalaica (Edgew.) Heimerl is among the most important genuine medicinal plants in Tibet. However, the biosynthesis mechanisms of the active compounds in this species are unclear, severely limiting its application. To clarify the molecular biosynthesis mechanism of the key representative active compounds, specifically rotenoid, which is of special medicinal value for M. himalaica, RNA sequencing and TOF-MS technologies were used to construct transcriptomic and metabolomic libraries from the roots, stems, and leaves of M. himalaica plants collected from their natural habitat. As a result, each of the transcriptomic libraries from the different tissues was sequenced, generating more than 10 Gb of clean data ultimately assembled into 147,142 unigenes. In the three tissues, metabolomic analysis identified 522 candidate compounds, of which 170 metabolites involved in 114 metabolic pathways were mapped to the KEGG. Of these genes, 61 encoding enzymes were identified to function at key steps of the pathways related to rotenoid biosynthesis, where 14 intermediate metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to rotenoid biosynthesis were synthesized in the roots, stems and leaves of M. himalaica, which suggested that the use of non-medicinal tissues to extract compounds was feasible. In addition, the CHS and CHI genes were found to play important roles in rotenoid biosynthesis, especially, since CHS might be an important rate-limiting enzyme. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of rotenoid in M. himalaica.Electronic supplementary materialThe online version of this article (10.1007/s00438-017-1409-y) contains supplementary material, which is available to authorized users.

Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation

“…All the results suggest that UV-B radiation improves the biosynthesis of rotenoid, a medicinal active ingredient of M. himalaica , which is mainly achieved by a series of regulatory activities induced by the PI signaling system and hormone signaling to promote the up-regulation of CHS . This result is consistent with previous studies that showed CHS is a key gene for rotenoid biosynthesis in M. himalaica [ 58 , 59 ].…”

“…It is possible that the metabolic activities of M. himalaica are significantly enhanced under the UV-B radiation, and M. himalaica adapts to UV-B radiation by increasing the ultraviolet-absorbing substance. Rotenoid, an important medicinal active ingredient in M. himalaica , is one of the downstream products of flavonoid metabolism [ 58 , 59 ]. Previous studies on rotenoid have been focused extensively on its anti-cancer activity and the treatment of leukemia [ 60 , 61 , 62 ].…”

“…Quantitative real-time PCR (qRT-PCR) was conducted using SYBR premix Ex Taq (Takara, Tokyo, Japan). The analyses were carried out in accordance with the procedures described by Gu et al [ 58 ] but with an annealing temperature of 62 °C. The 18S gene was selected as an internal control for normalizing the expression of the genes detected; the expression levels of this gene were more stable than those of the transcripts among the samples [ 58 ].…”

Rumen and plasma metabolomics profiling by UHPLC-QTOF/MS revealed metabolic alterations associated with a high-corn diet in beef steers

“…Collision energy (CE) was 30 V (15 MS/MS events with a production accumulation time of 50 msec each). The parameters of the electron spray ionization (ESI) source were set as follows: ion source gas 1 as 60 psi, ion source gas 2 as 60 psi, curtain gas as 35 psi, source temperature 650°C, and ion spray voltage floating (ISVF) 5000 V or -4000 V in positive or negative mode, respectively [20, 21].…”

Integrated metabolomic and transcriptomic analyses identify critical genes in eicosapentaenoic acid biosynthesis and metabolism in the sea urchin Strongylocentrotus intermedius

“…For instance, the transcriptomes throughout embryonic development of Strongylocentrotus purpuratus using RNA-seq were analyzed to understand the global gene regulatory networks during the embryonic development of sea urchins 17 ; a comparative transcriptome analysis of different colored tube feet in Strongylocentrotus intermedius was conducted to understand the differences at the molecular level and provide valuable information for marker-assisted breeding in this species 18 ; nuclear magnetic resonance (NMR)-based metabolomics was applied to embryos of the sea urchin Arbacia lixula to reveal the effects of decreased levels of choline and N-acetyl serotonin on the cholinergic and serotoninergic system 19 ; the metabolomic and de novo transcriptomic methods were used to investigate the reproductive success of the sea urchin Paracentrotus lividus which fed on two abundantly occurring benthic diatoms 20 . The integration of both metabolomics and transcriptomics is a powerful tool for revealing the biosynthetic mechanisms of key metabolic pathways 21 . Therefore, such studies can be used as an initial step to investigate the critical genes and the process of PUFA biosynthesis and metabolism in the sea urchin.…”