CN105671159A - Method for screening notoginsenoside synthesis key genes based on metabolites and gene expression - Google Patents

Method for screening notoginsenoside synthesis key genes based on metabolites and gene expression Download PDF

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CN105671159A
CN105671159A CN201610114420.1A CN201610114420A CN105671159A CN 105671159 A CN105671159 A CN 105671159A CN 201610114420 A CN201610114420 A CN 201610114420A CN 105671159 A CN105671159 A CN 105671159A
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saponin
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radix notoginseng
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齐炼文
陆续
王宁
李萍
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China Pharmaceutical University
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Abstract

The invention discloses a method for screening notoginsenoside synthesis key genes based on metabolites and gene expression. The method specifically comprises the following steps: analyzing metabolite contents of different parts of annual panax notoginseng by adopting a high performance liquid chromatography-mass spectrometry combination system, meanwhile quantitatively analyzing the expression quantity of saponin synthesis route key enzyme genes by using a fluorescent quantitation PCR technology, building a gene-metabolite correlation diagram by canonical correlation analysis, and screening key genes. Important information is provided for further illustrating a synthesis mechaism of saponin matters in the panax notoginseng, and meanwhile an importance basis is provided for improving the content of notoginsenoside by means of gene control and the like.

Description

Based on the method that metabolite and gene expression screen arasaponin synthesis key gene
Technical field
The present invention relates to the screening of triterpene saponin route of synthesis key gene in Radix Notoginseng, particularly carry out typical case's association analysis (canonicalcorrelationanalysis) in conjunction with the expression of annual Radix Notoginseng metabolite content and triterpene saponin route of synthesis key gene, filter out triterpene saponin route of synthesis key gene in Radix Notoginseng, saponin content contribution degree is bigger.
Background technology
Radix Notoginseng (Panaxnotoginseng (Burk.) F.H.Chen) is araliaceae ginseng plant, is China's tradition valuable ingredient of Chinese medicine, and its major physiological active component is arasaponin. The ancient times that are applied in of Radix Notoginseng create key medicine mainly as gold, and traumatic injury, the stasis of blood stagnant treatment swollen and ache various hemorrhage for inside and outside. Modern pharmacology research shows that Radix Notoginseng total arasaponins and partial monosomy saponin all have good physiologically active in blood and cardiovascular system, systemic metabolism, immunity and antiinflammatory, antitumor etc., and its many-sided pharmacological action and health care are increasingly subject to people's attention. The main source of current arasaponin extracts from cultivation Radix Notoginseng and obtains, but Radix Notoginseng is herbaceos perennial, growth cycle is long, and growth conditions is harsh, geographical distribution is narrow, in addition the problem such as pest and disease damage serious, continuous cropping obstacle, pesticide residues, its yield has been difficult to meet the market demand quickly increased.
In recent years, the focus of molecular biology research has been become for the gene regulation of medicinal plants secondary metabolite, and saponins material is the important component part of Secondary metabolites, its content and composition depend primarily on biosynthesis key gene expression in cell. In plant cell, terpenoid is mainly derived from two precursor substances, isopentenyl pyrophosphate (IPP) and isomer dimethylallylpyrophosphate (DMAPP) thereof. Mevalonic acid (MVA) approach in Cytoplasm and the 2-C-methyl D in plastid-erythritol-4-phosphoric acid (MEP) approach can both produce IPP and DMAPP, and IPP produced by two approach can pass used by plastid film the other side each other. IPP molecule and two DMAPP molecules generate farnesyl pyrophosphate (FPP) under the effect of farnesyl pyrophosphate synthase (FPS), and two FPP molecules generate the precursor zamene of triterpene substance under the effect of squalene synthase (SQS) with head-head mode reductive coupling. Subsequently, zamene is oxidized to 2,3-oxidosqualene under the effect of squalene epoxidase (SE), and dammarane's glycol synzyme (DS) catalysis 2,3-oxidosqualene cyclisation is dammarendiol.Dammarendiol is the skeleton of dammarane type four-ring triterpenoid saponin class, ultimately forms different types of dammarane type four-ring triterpenoid saponin under the effect of cytochrome P 450 monooxygenases and multiple glycosyl transferase. At present, clone and the qualification in panax species of some key genes in plant triterpene saponin formation approach, research confirms that triterpene saponin synthesis is played important regulating and controlling effect by their expression. Additionally, the genes such as FPS, SS, SE and DS have been analyzed by Niu et al. in the expression in 4 years raw sangqi ginseng florescence, lay the foundation for being further elucidated with saponins material synthesis mechanism in Radix Notoginseng.
The present invention synthesizes the relatedness of key gene expression and metabolite content for starting point to explore triterpene saponin in Radix Notoginseng, the metabolite content of annual Radix Notoginseng different parts has been analyzed by application HPLC-MS system, utilize fluorescent quantitative PCR technique that its saponin formation pathway key enzyme gene expression amount is carried out quantitative analysis simultaneously, and construct the relevant figure of Radix Notoginseng gene-metabolite by typical case's association analysis, key gene has been screened. Before making the present invention, not yet go out to now refer to, based on triterpene saponin content and route of synthesis key gene expression thereof, Radix Notoginseng triterpene saponin is synthesized the open report that key gene screens.
Summary of the invention
It is an object of the invention to build Panax notoginseng Growth and grow the relational network of early stage saponin formation key gene and metabolite content, the key gene in screening Radix Notoginseng plant, saponin formation played an important role.
In order to realize foregoing invention purpose, technical scheme provided by the invention comprises the following steps:
1) annual Radix Notoginseng different parts saponins substance metabolism profile is analyzed.
2) expression at Radix Notoginseng different parts of the saponin formation pathway key gene is measured.
3) gene-metabolite relational network is built, saponin formation key gene in screening Radix Notoginseng.
In said method, described Radix Notoginseng different parts is the leaf of annual Radix Notoginseng, petiole and root.
Step 1) described analysis saponins substance metabolism profile be adopt HPLC-MS system different parts sample methanolic extract is detected, use internal standard method undertaken quantitatively by standard curve. Analysis method is with reference to the saponin quantitative approach of report in Li et al. " GlobalanalysisofchemicalconstituentsinShengmaiinjectionu singhighperformanceliquidchromatographycoupledwithtandem massspectrometry " paper.
Step 2) described Radix Notoginseng different parts saponin formation pathway key gene expression adopt quantitative fluorescent PCR (RT-Q-PCR) technology detect. Specifically extract sample RNA respectively, then RNA reverse transcription is synthesized the first chain cDNA, with cDNA for template, according to Takara company SYBRPremixExTaqTMIn description forThe method that 96 real-time fluorescence quantitative PCR instrument are recommended is configured.
Specific primer particular sequence in the reaction of above-mentioned quantitative fluorescent PCR is referring to table 1.
The gene primer sequence used in table 1RT-Q-PCR
The reaction condition of described real-time fluorescence quantitative PCR detection is: 95 DEG C of denaturation 2min, 95 DEG C of degeneration 10s, and 57 DEG C of annealing 15s, 72 DEG C extend 30s, 45 circulations.
Step 3) described in the structure of gene-metabolite relational network and the screening of biosynthesis key gene combine with saponin formation pathway key gene expression to analyze by arasaponin content by typical case's association analysis and obtain.Particularly using Pearson's correlation coefficient that the expression of saponin content and saponin formation pathway key gene is carried out canonical correlation analysis, variant correlation coefficient is higher than 0.5 as the standard screening crucial synthetic gene.
The present invention constructs gene-metabolite relational network based on the expression of saponins substance metabolism and saponin formation pathway key gene in annual Radix Notoginseng, Panax notoginseng Growth initial stage saponin formation key gene has been screened, in order to be further elucidated with in Radix Notoginseng, saponins material synthesis mechanism provides important information, simultaneously for providing important evidence by means raising arasaponin content such as gene regulations.
Accompanying drawing explanation
Fig. 1 is triterpene saponin material route of synthesis in vivo;
Fig. 2 is annual Radix Notoginseng different parts saponins substance metabolism profile spectrogram, and wherein A is standard substance mixed solutions, and B is annual Folium Notoginseng, and C is annual Radix Notoginseng, and D is annual Radix Notoginseng petiole;
Fig. 3 is that saponin is at different parts distribution and content thermal map;
Fig. 4 is annual Radix Notoginseng different parts saponin content PCA analysis chart, and wherein 1 is annual Radix Notoginseng, and 2 is annual Radix Notoginseng petiole, and 3 is annual Folium Notoginseng;
Fig. 5 is the expression in annual Radix Notoginseng different parts of the saponin formation pathway key gene;
Fig. 6 is annual Radix Notoginseng gene-metabolite relational network.
Detailed description of the invention
Below embodiments of the invention being elaborated, following example will assist in those skilled in the art and are further appreciated by the present invention, but do not limit the present invention in any form. Experimental technique in following embodiment, if no special instructions, is conventional method. Reagent used in following embodiment if no special instructions, is commercially available purchase product.
Embodiment 1: metabolic profiling analysis.
1) materials and methods
Vegetable material used comes from this laboratory cultivation Radix Notoginseng, and Panax notoginseng seeds is purchased from Wenshan Prefecture of Yunnan Province, is seeded in greenhouse in December, 2013, in strict accordance with notoginseng planting standard, it is ensured that the shady and cool lucifuge of Panax notoginseng Growth environment and suitable humiture. June in the coming year, the leaf of annual Radix Notoginseng plant, petiole and root being drawn materials respectively, sample is after liquid nitrogen flash freezer, and freezen protective is in-80 DEG C of refrigerators.
2) sample extraction
By each sample grind into powder, with methanol, sample is extracted after the lyophilization of 48 hours. Precise 50mg sample is dissolved in 1.5mL methanol, vortex 1min, room temperature supersound extraction half an hour, gained mixed solution overnight stand, 12000rmp centrifuging and taking supernatant. Residue methanol extracts again, supersound process 1 hour, centrifugal, and the supernatant of two times centrifugal is mixed for the mensuration of saponin content. Root and petiole extract dilute 2 times, and leaf extract dilutes 5 times, through 0.22 μm of organic membrane filtration before all samples sample introduction.
3) saponin metabolic profiling analysis
With reference to Li et al. saponin quantitative approach of report in " GlobalanalysisofchemicalconstituentsinShengmaiinjectionu singhighperformanceliquidchromatographycoupledwithtandem massspectrometry " paper, HPLC-MS technology is adopted to be analyzed above-mentioned sample extraction thing obtaining different parts metabolic profile spectrum.
Instrumental Analysis platform used is Agilent1100seriesLC/MSDtrapsystem.
Chromatographic condition: separation chromatography post is AgilentzorbaxSB-C18 chromatographic column (4.6mm × 250mm, 5 μm), separation condition is: column temperature 30 DEG C, flow velocity 1mL/min, mobile phase forms 0.1% aqueous formic acid (A) and 0.1% formic acid acetonitrile solution (B), sample size is 10 μ L, gradient elution program is as follows: 0-5min is 25%B, 5-10min is 25-32%B, 10-35min is 32%B, 35-40min be 32-37%B, 40-44min is 37%B, 44-45min is 37-75%B, 45-55min is 75%B.
Mass Spectrometry Conditions: adopt API-ES negative ion mode to detect, with nitrogen as dry gas, assisted gas.Dry temperature is set as 350 DEG C, and flow velocity is 9mL/min, and capillary voltage and collision voltage are respectively set as 350V and 120V, and assisted gas pressure is 40psig. Spectrum data collection adopts selected ion monitoring (SIM) pattern to carry out.
Different parts respectively takes 3 different samples and is measured, and is calculated the content of each saponin by standard curve with internal standard method, and result SIMCA-Psoftware11.5 carries out PCA analysis.
Embodiment 2 gene expression analysis.
Saponin formation pathway key gene expression detection by quantitative
The RNApreppureplantkit description extracting reference BioTeke company of sample total serum IgE, detects the integrity of carried RNA with 1% agarose gel electrophoresis after extraction, measure the value of OD260/OD280 and OD260/OD230, the purity of detection RNA and concentration. The synthesis of cDNA the first chain is with reference to PrimeScriptRTreagentkit (Takara) description. Subsequently, with cDNA the first chain for template, adoptSaponin formation pathway key gene FPS, SQS, DS, SE and CYP716A53 in annual Radix Notoginseng are carried out relative quantitative assay by 96 real-time fluorescence quantitative PCR instrument. Quantitative PCR is according to SYBRPremixExTaqTM(Takara) operation instruction preparation reaction system, wherein each gene specific upstream and downstream primer utilizes PrimerPremier5.0 software design according to the conservative region of Radix Notoginseng corresponding gene fragment, Jiangsu Jin Weizhi company synthesize, and particular sequence is referring to table 1. The reaction condition of real-time fluorescence quantitative PCR detection is: 95 DEG C of denaturation 2min, 95 DEG C of degeneration 10s, and 57 DEG C of annealing 15s, 72 DEG C extend 30s, 45 circulations. Select actin as reference gene, calculate each gene relative expression quantity in different parts according to Ct value.
The structure of embodiment 3 genes-metabolite relational network.
It is associated analyzing by the expression of saponin formation pathway key gene in the saponin content to annual Radix Notoginseng of the Pearson's correlation coefficient in typical case association analysis (canonicalcorrelationanalysis) and different parts, building annual Radix Notoginseng gene-metabolite relational network, screening wherein synthesizes, for arasaponin, the gene that contribution degree is bigger. Variant correlation coefficient cut off value for key gene screening is 0.5.
Result and analysis
Annual Radix Notoginseng different parts saponin content difference
As shown in Figures 2 and 3, all there is significant difference in annual Radix Notoginseng different parts saponins substance metabolism spectrogram and saponin distribution. It addition, as shown in table 2, each saponin content and saponin content summation are also different in different parts sample. In Folium Notoginseng, total saponin content is the highest, respectively 3 times and 8.5 times of root and petiole total saponin content. Root sample is then mainly made up of protopanaxadiol-type's saponin containing abundant protopanoxadiol and Protopanaxatriol's type saponin, leaf and petiole part, contains only a small amount of ginsenoside Re, point out annual Radix Notoginseng Central Plains protopanaxatriol ginsenoside mainly to synthesize at root. Ginsenoside Rc, Rb2And Rb3The summation of three kinds of saponin contents has reached the 90% of total saponin content in leaf, and its ratio of saponin total content shared by root and petiole is less than 10%. Radix Ginseng peculiar saponin ginsenoside R1 only detects at the root of annual Radix Notoginseng. In addition, oleanolic acid type saponin ginsenoside Ro and the Rhizoma Panacis Japonici saponin Iva of trace is also detected that at the root of annual Radix Notoginseng.
The annual Radix Notoginseng different parts saponin content of table 2
Note: unit is μ g/mL, standard error comes from three independent biological repetitions, and nd shows to be not detected by.
Principal component analysis (PCA)
As shown in Figure 4, annual Radix Notoginseng each position saponin component is widely different, and they are substantially distributed in zones of different, root and leaf and petiole and reach to be kept completely separate by main constituent 1, and leaf and petiole sample are then substantially distinguished by main constituent 2.
The expression in annual Radix Notoginseng of the saponin formation pathway key gene
As it is shown in figure 5, saponin formation pathway key gene FPS, SQS, DS, SE and CYP716A53 are in the expression difference to some extent of annual Radix Notoginseng different parts. SQS expression in leaf is the highest, takes second place in petiole, and in root, expression is minimum. Tri-genes of FPS, DS, SE are similar at the expression pattern of Different Organs, gene expression amount be all according to leaf, root, petiole decreasing order, and the expression that FPS is in root and petiole is higher compared to DS and SE. CYP716A53 expression in Different Organs is substantially the same. Five kinds of genes expression in leaf is all of a relatively high, and the result of saponin content high with leaf is consistent.
The screening of saponin formation key gene in Radix Notoginseng
As shown in Figure 6, using Pearson's correlation coefficient that the expression of saponin content and saponin formation pathway key gene is carried out canonical correlation analysis, build annual Radix Notoginseng gene-metabolite relational network, screening is wherein for gene that saponin formation contribution degree is bigger. Variant correlation coefficient cut off value 0.5 is for the screening of key gene, it is shown that FPS, SQS, DS, SE gene and Ginsenoside Rc, Rb2And Rb3Synthesis dependency relatively big, SQS also with ginsenoside Rb1Synthesis be correlated with. Filtered out to ginsenoside Rb2, the gene that Rb3 and Rc synthesis plays an important role is arranged as SE > DS > SQS > FPS according to its contribution degree order of variant correlation coefficient size.
Saponins substance metabolism is connected by this research with the expression of key gene on its route of synthesis, build annual Radix Notoginseng gene-metabolite relational network, and then filter out arasaponin is synthesized the bigger gene of contribution degree, for the illustrating and have important reference by means raising arasaponin content such as gene regulations of saponins material synthesis mechanism in Radix Notoginseng from now on.

Claims (7)

1. the method screening arasaponin synthesis key gene based on metabolite and gene expression, it is characterised in that comprise the steps:
(1) Radix Notoginseng different parts triterpene saponin substance metabolism profile is analyzed;
(2) the saponin formation pathway key gene express spectra at Radix Notoginseng different parts is analyzed;
(3) build gene expression figure relevant with the metabolism of saponin, filter out saponin formation key gene in Radix Notoginseng.
2. method according to claim 1, it is characterised in that: described metabolic profile adopts HPLC-MS system to carry out, and described express spectra adopts quantitative fluorescent PCR to carry out, and described relevant figure adopts typical case's association analysis to carry out.
3. method according to claim 1, described different parts includes: leaf, petiole and root.
4. method according to claim 1, described key gene includes: farnesyl pyrophosphate synthase (FPS), squalene synthase (SQS), squalene epoxidase (SE), dammarane's glycol synzyme (DS), Cytochrome P450 oxidase (CYP716A53).
5. method according to claim 2, is further characterized in that the methanolic extract of Radix Notoginseng sample is analyzed by employing HPLC-MS system.
6. method according to claim 2, sample RNA is specifically extracted in described quantitative analysis respectively, then RNA reverse transcription synthesizes the first chain cDNA, with cDNA for template, carries out real-time fluorescence quantitative PCR.
7. method according to claim 1, it is characterized in that the structure of the dependency relation network figure of the gene expression amount described in step (3) and saponin metabolism amount, by typical case's association analysis, arasaponin content is combined with saponin formation pathway key gene expression and analyze and obtain, specifically using Pearson's correlation coefficient that saponin content and saponin formation pathway key gene expression are carried out canonical correlation analysis, variant correlation coefficient is higher than 0.5 as the standard screening crucial synthetic gene.
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CN107247889A (en) * 2017-05-12 2017-10-13 清华大学 The error method for improving analyzed for gene association on uneven sample
CN108103176A (en) * 2018-01-02 2018-06-01 中国药科大学 Method based on metabolism group and transcription group association analysis screening fritillaria alkaloid synthesis key gene
CN109402164A (en) * 2018-11-21 2019-03-01 中国农业科学院北京畜牧兽医研究所 A kind of alfalfa is overexpressed the method and application of squalene epoxidase enzyme gene
CN109613157A (en) * 2018-11-27 2019-04-12 山东万邦赛诺康生化制药股份有限公司 A kind of raw material heparin sodium for producing Enoxaparin Sodium and using
CN109694903A (en) * 2019-01-09 2019-04-30 中国药科大学 The method for synthesizing key gene with gene expression association analysis screening ginkgolides based on ginkgolides content
CN113796275A (en) * 2021-09-22 2021-12-17 昆明理工大学 Method for promoting growth of panax notoginseng plant and synthesis of saponin and application thereof
CN115725620A (en) * 2022-09-12 2023-03-03 昆明理工大学 Method for synthesizing panax japonicus saponin in panax notoginseng cells

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Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107247889A (en) * 2017-05-12 2017-10-13 清华大学 The error method for improving analyzed for gene association on uneven sample
CN108103176A (en) * 2018-01-02 2018-06-01 中国药科大学 Method based on metabolism group and transcription group association analysis screening fritillaria alkaloid synthesis key gene
CN109402164A (en) * 2018-11-21 2019-03-01 中国农业科学院北京畜牧兽医研究所 A kind of alfalfa is overexpressed the method and application of squalene epoxidase enzyme gene
CN109613157A (en) * 2018-11-27 2019-04-12 山东万邦赛诺康生化制药股份有限公司 A kind of raw material heparin sodium for producing Enoxaparin Sodium and using
CN109694903A (en) * 2019-01-09 2019-04-30 中国药科大学 The method for synthesizing key gene with gene expression association analysis screening ginkgolides based on ginkgolides content
CN113796275A (en) * 2021-09-22 2021-12-17 昆明理工大学 Method for promoting growth of panax notoginseng plant and synthesis of saponin and application thereof
CN115725620A (en) * 2022-09-12 2023-03-03 昆明理工大学 Method for synthesizing panax japonicus saponin in panax notoginseng cells
CN115725620B (en) * 2022-09-12 2023-09-15 昆明理工大学 Method for synthesizing panax japonicus saponins in pseudo-ginseng cells

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