Application in medicinal plants research by high-throughput metabolomics method

GUO Zhiying; ZHOU Zheng; TAN Hexin; ZHANG Lei; DIAO Yong

doi:10.3969/j.issn.1006-0111.2017.06.005

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Article Navigation > Journal of Pharmaceutical Practice and Service > 2017 > 35(6): 499-503

GUO Zhiying, ZHOU Zheng, TAN Hexin, ZHANG Lei, DIAO Yong. Application in medicinal plants research by high-throughput metabolomics method[J]. Journal of Pharmaceutical Practice and Service, 2017, 35(6): 499-503. doi: 10.3969/j.issn.1006-0111.2017.06.005

Citation:

GUO Zhiying, ZHOU Zheng, TAN Hexin, ZHANG Lei, DIAO Yong. Application in medicinal plants research by high-throughput metabolomics method[J]. Journal of Pharmaceutical Practice and Service, 2017, 35(6): 499-503. doi: 10.3969/j.issn.1006-0111.2017.06.005

Application in medicinal plants research by high-throughput metabolomics method

doi: 10.3969/j.issn.1006-0111.2017.06.005

1.
School of Biomedical Science, Huaqiao University, Quanzhou, 362021, China;Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
2.
Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
3.
School of Biomedical Science, Huaqiao University, Quanzhou, 362021, China

Received Date: 2017-07-15
Rev Recd Date: 2017-09-15

Abstract

High-throughput metabolomics have developed very rapidly in recent years and been widely used in medicinal plants research. At present, high-throughput metabolomics mainly applied in the following areas, quality control of medicinal plants by fingerprints, metabolites difference comparison before and after genetic engineering, monitoring metabolites change in different environment and gene function study. High-throughput metabolomics have a great future, but still have some challenges, such as the requirements for more sophisticated equipment and complexity of data integration. With the advancement of science and technology, high-throughput metabolomics will be an irreplaceable tool for the research of medicinal plants.
- high-throughput metabolomics,
- medicinal plants,
- quality control,
- data integration

References

[1]	Nielsen J. Systems Biology of Metabolism[J]. Annu Rev Biochem, 2017, 86:245-275.
[2]	Fiehn O. Metabolomics-the link between genotypes and phenotypes[J]. Plant Mol Biol, 2002, 48(1-2):155-171.
[3]	Karahalil B. Overview of Systems Biology and Omics Technologies[J]. Curr Med Chem, 2016, 23(37):4221-4230.
[4]	Petersson SV, Lindén P, Moritz T,et al. Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology[J]. Metabolomics, 2015, 11(6):1679-1689.
[5]	Danielsson AP, Moritz T, Mulder H,et al. Development and optimization of a metabolomic method for analysis of adherent cell cultures[J]. Anal Biochem, 2010, 404(1):30-39.
[6]	Wolfender JL, Glauser G, Boccard J,et al. MS-based plant metabolomic approaches for biomarker discovery[J]. Nat Prod Commun, 2009, 4(10):1417-1430.
[7]	Ramautar R, Somsen GW, de Jong G J. CE-MS for metabolomics:Developments and applications in the period 2014-2016[J]. Electrophoresis, 2017, 38(1):190-202.
[8]	Tohge T, Fernie AR. Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function[J]. Nat Protoc, 2010, 5(6):1210-1227.
[9]	Ernst M, Silva DB, Silva RR,et al. Mass spectrometry in plant metabolomics strategies:from analytical platforms to data acquisition and processing[J]. Nat Prod Rep, 2014, 31(6):784-806.
[10]	Mak TD, Laiakis EC, Goudarzi M,et al. MetaboLyzer:a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data[J]. Anal Chem, 2014, 86(1):506-513.
[11]	Culibrk L, Croft CA, Tebbutt SJ, et al. Systems Biology Approaches for Host-Fungal Interactions:An Expanding Multi-Omics Frontier[J]. OMICS, 2016, 20(3):127-138.
[12]	Wan JY, Liu P, Wang HY, et al. Biotransformation and metabolic profile of American ginseng saponins with human intestinal microflora by liquid chromatography quadrupole time-of-flight mass spectrometry[J]. J Chromatogr A, 2013, 1286:83-92.
[13]	Kim N, Kim K, Lee D,et al. Nontargeted metabolomics approach for age differentiation and structure interpretation of age-dependent key constituents in hairy roots of Panax ginseng[J]. J Nat Prod, 2012, 75(10):1777-1784.
[14]	Park HE, Lee SY, Hyun SH,et al. Gas chromatography/mass spectrometry-based metabolic profiling and differentiation of ginseng roots according to cultivation age using variable selection[J]. J AOAC Int, 2013, 96(6):1266-1272.
[15]	Chu C, Xu S, Li X,et al. Profiling the ginsenosides of three ginseng products by LC-Q-TOF/MS[J]. J Food Sci, 2013, 78(5):C653-C659.
[16]	Kim SH, Hyun SH, Yang SO,et al. (1)H-NMR-based discrimination of thermal and vinegar treated ginseng roots[J]. J Food Sci, 2010, 75(6):C577-C581.
[17]	Lee EJ, Shaykhutdinov R, Weljie AM,et al. Quality assessment of ginseng by (1)H NMR metabolite fingerprinting and profiling analysis[J]. J Agric Food Chem, 2009, 57(16):7513-7522.
[18]	Li SL, Song JZ, Choi FF,et al. Chemical profiling of Radix Paeoniae evaluated by ultra-performance liquid chromatography/photo-diode-array/quadrupole time-of-flight mass spectrometry[J]. J Pharm Biomed Anal, 2009, 49(2):253-266.
[19]	Montoro P, Maldini M, Piacente S,et al. Metabolite fingerprinting of Camptotheca acuminata and the HPLC-ESI-MS/MS analysis of camptothecin and related alkaloids[J]. J Pharm Biomed Anal, 2010, 51(2):405-415.
[20]	Pan Q, Wang Q, Yuan F,et al. Overexpression of ORCA3 and G10H in Catharanthus roseus plants regulated alkaloid biosynthesis and metabolism revealed by NMR-metabolomics[J]. PLoS One, 2012, 7(8):e43038.
[21]	Dai H, Xiao C, Liu H,et al. Combined NMR and LC-MS analysis reveals the metabonomic changes in Salvia miltiorrhiza Bunge induced by water depletion[J]. J Proteome Res, 2010, 9(3):1460-1475.
[22]	Yamazaki M, Mochida K, Asano T,et al. Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones[J]. Plant Cell Physiol, 2013, 54(5):686-696.
[23]	Chen J, Dong X, Li Q,et al. Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling[J]. BMC Genomics, 2013, 14(1):857.
[24]	Toh DF, New LS, Koh HL,et al. Ultra-high performance liquid chromatography/time-of-flight mass spectrometry (UHPLC/TOFMS) for time-dependent profiling of raw and steamed Panax notoginseng[J]. J Pharm Biomed Anal, 2010, 52(1):43-50.
[25]	Bondia-Pons I, Savolainen O, Törrönen R, et al. Metabolic profiling of Goji berry extracts for discrimination of geographical origin by non-targeted liquid chromatography coupled to quadrupole time-of-flight massspectrometry[J]. Food Res Int, 2014, 63:132-138.
[26]	Duan LX, Chen TL, Li M,et al. Use of the metabolomics approach to characterize Chinese medicinal material Huangqi[J]. Mol Plant, 2012, 5(2):376-386.
[27]	Jung JY, Jung Y, Kim JS,et al. Assessment of peeling of Astragalus roots using 1H NMR-and UPLC-MS-based metabolite profiling[J]. J Agric Food Chem, 2013, 61(43):10398-10407.
[28]	Kwon J, Kim N, Lee D,et al. Metabolomics approach for the discrimination of raw and steamed Gastrodia elata using liquid chromatography quadrupole time-of-flight mass spectrometry[J]. J Pharm Biomed Anal, 2014, 94:132-138.
[29]	de Oliveira Dal'Molin Cristiana G, Orellana Camila, Gebbie Leigh,et al. Metabolic reconstruction of setaria italica:A systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses[J]. Front Plant Sci, 2016, 7:1138.
[30]	Murch SJ, Rupasinghe HP, Goodenowe D,et al. A metabolomic analysis of medicinal diversity in Huang-qin (Scutellaria baicalensis Georgi) genotypes:discovery of novel compounds[J]. Plant Cell Rep, 2004, 23(6):419-425.
[31]	Kim HK, Choi YH, Erkelens C,et al. Metabolic fingerprinting of Ephedra species using ¹H-NMR spectroscopy and principal component analysis[J]. Chem Pharm Bull (Tokyo), 2005, 53(1):105-109.
[32]	Li SL, Shen H, Zhu LY,et al. Ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry based chemical profiling approach to rapidly reveal chemical transformation of sulfur-fumigated medicinal herbs, a case study on white ginseng[J]. J Chromatogr A, 2012, 1231:31-45.
[33]	Lee EJ, Shaykhutdinov R, Weljie AM,et al. Quality assessment of ginseng by1H-NMR metabolite fingerprinting and profiling analysis[J]. J Agric Food Chem, 2009, 57(16):7513-7522.
[34]	Winzer T, Gazda V, He Z,et al. A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine[J]. Science, 2012, 336(6089):1704-1708.
[35]	Happyana N, Kayser O. Monitoring metabolite profiles of Cannabis sativa L. Trichomes during flowering period using ¹H NMR-based metabolomics and real-time PCR[J]. Planta Med, 2016, 82(13):1217-1223.
[36]	Jia X, Sun C, Zuo Y,et al. Integrating transcriptomics and metabolomics to characterise the response of Astragalus membranaceus Bge. var. mongolicus (Bge.) to progressive drought stress[J]. BMC Genomics, 2016, 17(1):88.
[37]	Guldbrandsen N, Kostidis S, Schäfer H,et al. NMR-based metabolomic study on isatis tinctoria:comparison of different accessions, harvesting dates, and the effect of repeated harvesting[J]. J Nat Prod, 2015, 78(5):977-986.
[38]	Goossens A. It is easy to get huge candidate gene lists for plant metabolism now, but how to get beyond?[J]. Mol Plant, 2015, 8(1):2-5.
[39]	Tian L, Hu Y, Chen XY. Advancing human health through exploration of plant metabolism and reaping the benefits of edible medicinal plants[J]. Mol Plant, 2017, 10(3):533-536.
[40]	Wurtzel ET, Kutchan TM. Plant metabolism, the diverse chemistry set of the future[J]. Science, 2016, 353(6305):1232-1236.

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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

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Application in medicinal plants research by high-throughput metabolomics method

1. School of Biomedical Science, Huaqiao University, Quanzhou, 362021, China;Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China

2. Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China

3. School of Biomedical Science, Huaqiao University, Quanzhou, 362021, China

Received Date: 2017-07-15

Rev Recd Date: 2017-09-15

Key words:

Abstract: High-throughput metabolomics have developed very rapidly in recent years and been widely used in medicinal plants research. At present, high-throughput metabolomics mainly applied in the following areas, quality control of medicinal plants by fingerprints, metabolites difference comparison before and after genetic engineering, monitoring metabolites change in different environment and gene function study. High-throughput metabolomics have a great future, but still have some challenges, such as the requirements for more sophisticated equipment and complexity of data integration. With the advancement of science and technology, high-throughput metabolomics will be an irreplaceable tool for the research of medicinal plants.

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Reference (40)

[1]	Nielsen J. Systems Biology of Metabolism[J]. Annu Rev Biochem, 2017, 86:245-275.
[2]	Fiehn O. Metabolomics-the link between genotypes and phenotypes[J]. Plant Mol Biol, 2002, 48(1-2):155-171.
[3]	Karahalil B. Overview of Systems Biology and Omics Technologies[J]. Curr Med Chem, 2016, 23(37):4221-4230.
[4]	Petersson SV, Lindén P, Moritz T,et al. Cell-type specific metabolic profiling of Arabidopsis thaliana protoplasts as a tool for plant systems biology[J]. Metabolomics, 2015, 11(6):1679-1689.
[5]	Danielsson AP, Moritz T, Mulder H,et al. Development and optimization of a metabolomic method for analysis of adherent cell cultures[J]. Anal Biochem, 2010, 404(1):30-39.
[6]	Wolfender JL, Glauser G, Boccard J,et al. MS-based plant metabolomic approaches for biomarker discovery[J]. Nat Prod Commun, 2009, 4(10):1417-1430.
[7]	Ramautar R, Somsen GW, de Jong G J. CE-MS for metabolomics:Developments and applications in the period 2014-2016[J]. Electrophoresis, 2017, 38(1):190-202.
[8]	Tohge T, Fernie AR. Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function[J]. Nat Protoc, 2010, 5(6):1210-1227.
[9]	Ernst M, Silva DB, Silva RR,et al. Mass spectrometry in plant metabolomics strategies:from analytical platforms to data acquisition and processing[J]. Nat Prod Rep, 2014, 31(6):784-806.
[10]	Mak TD, Laiakis EC, Goudarzi M,et al. MetaboLyzer:a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data[J]. Anal Chem, 2014, 86(1):506-513.
[11]	Culibrk L, Croft CA, Tebbutt SJ, et al. Systems Biology Approaches for Host-Fungal Interactions:An Expanding Multi-Omics Frontier[J]. OMICS, 2016, 20(3):127-138.
[12]	Wan JY, Liu P, Wang HY, et al. Biotransformation and metabolic profile of American ginseng saponins with human intestinal microflora by liquid chromatography quadrupole time-of-flight mass spectrometry[J]. J Chromatogr A, 2013, 1286:83-92.
[13]	Kim N, Kim K, Lee D,et al. Nontargeted metabolomics approach for age differentiation and structure interpretation of age-dependent key constituents in hairy roots of Panax ginseng[J]. J Nat Prod, 2012, 75(10):1777-1784.
[14]	Park HE, Lee SY, Hyun SH,et al. Gas chromatography/mass spectrometry-based metabolic profiling and differentiation of ginseng roots according to cultivation age using variable selection[J]. J AOAC Int, 2013, 96(6):1266-1272.
[15]	Chu C, Xu S, Li X,et al. Profiling the ginsenosides of three ginseng products by LC-Q-TOF/MS[J]. J Food Sci, 2013, 78(5):C653-C659.
[16]	Kim SH, Hyun SH, Yang SO,et al. (1)H-NMR-based discrimination of thermal and vinegar treated ginseng roots[J]. J Food Sci, 2010, 75(6):C577-C581.
[17]	Lee EJ, Shaykhutdinov R, Weljie AM,et al. Quality assessment of ginseng by (1)H NMR metabolite fingerprinting and profiling analysis[J]. J Agric Food Chem, 2009, 57(16):7513-7522.
[18]	Li SL, Song JZ, Choi FF,et al. Chemical profiling of Radix Paeoniae evaluated by ultra-performance liquid chromatography/photo-diode-array/quadrupole time-of-flight mass spectrometry[J]. J Pharm Biomed Anal, 2009, 49(2):253-266.
[19]	Montoro P, Maldini M, Piacente S,et al. Metabolite fingerprinting of Camptotheca acuminata and the HPLC-ESI-MS/MS analysis of camptothecin and related alkaloids[J]. J Pharm Biomed Anal, 2010, 51(2):405-415.
[20]	Pan Q, Wang Q, Yuan F,et al. Overexpression of ORCA3 and G10H in Catharanthus roseus plants regulated alkaloid biosynthesis and metabolism revealed by NMR-metabolomics[J]. PLoS One, 2012, 7(8):e43038.
[21]	Dai H, Xiao C, Liu H,et al. Combined NMR and LC-MS analysis reveals the metabonomic changes in Salvia miltiorrhiza Bunge induced by water depletion[J]. J Proteome Res, 2010, 9(3):1460-1475.
[22]	Yamazaki M, Mochida K, Asano T,et al. Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones[J]. Plant Cell Physiol, 2013, 54(5):686-696.
[23]	Chen J, Dong X, Li Q,et al. Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling[J]. BMC Genomics, 2013, 14(1):857.
[24]	Toh DF, New LS, Koh HL,et al. Ultra-high performance liquid chromatography/time-of-flight mass spectrometry (UHPLC/TOFMS) for time-dependent profiling of raw and steamed Panax notoginseng[J]. J Pharm Biomed Anal, 2010, 52(1):43-50.
[25]	Bondia-Pons I, Savolainen O, Törrönen R, et al. Metabolic profiling of Goji berry extracts for discrimination of geographical origin by non-targeted liquid chromatography coupled to quadrupole time-of-flight massspectrometry[J]. Food Res Int, 2014, 63:132-138.
[26]	Duan LX, Chen TL, Li M,et al. Use of the metabolomics approach to characterize Chinese medicinal material Huangqi[J]. Mol Plant, 2012, 5(2):376-386.
[27]	Jung JY, Jung Y, Kim JS,et al. Assessment of peeling of Astragalus roots using 1H NMR-and UPLC-MS-based metabolite profiling[J]. J Agric Food Chem, 2013, 61(43):10398-10407.
[28]	Kwon J, Kim N, Lee D,et al. Metabolomics approach for the discrimination of raw and steamed Gastrodia elata using liquid chromatography quadrupole time-of-flight mass spectrometry[J]. J Pharm Biomed Anal, 2014, 94:132-138.
[29]	de Oliveira Dal'Molin Cristiana G, Orellana Camila, Gebbie Leigh,et al. Metabolic reconstruction of setaria italica:A systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses[J]. Front Plant Sci, 2016, 7:1138.
[30]	Murch SJ, Rupasinghe HP, Goodenowe D,et al. A metabolomic analysis of medicinal diversity in Huang-qin (Scutellaria baicalensis Georgi) genotypes:discovery of novel compounds[J]. Plant Cell Rep, 2004, 23(6):419-425.
[31]	Kim HK, Choi YH, Erkelens C,et al. Metabolic fingerprinting of Ephedra species using ¹H-NMR spectroscopy and principal component analysis[J]. Chem Pharm Bull (Tokyo), 2005, 53(1):105-109.
[32]	Li SL, Shen H, Zhu LY,et al. Ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry based chemical profiling approach to rapidly reveal chemical transformation of sulfur-fumigated medicinal herbs, a case study on white ginseng[J]. J Chromatogr A, 2012, 1231:31-45.
[33]	Lee EJ, Shaykhutdinov R, Weljie AM,et al. Quality assessment of ginseng by1H-NMR metabolite fingerprinting and profiling analysis[J]. J Agric Food Chem, 2009, 57(16):7513-7522.
[34]	Winzer T, Gazda V, He Z,et al. A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine[J]. Science, 2012, 336(6089):1704-1708.
[35]	Happyana N, Kayser O. Monitoring metabolite profiles of Cannabis sativa L. Trichomes during flowering period using ¹H NMR-based metabolomics and real-time PCR[J]. Planta Med, 2016, 82(13):1217-1223.
[36]	Jia X, Sun C, Zuo Y,et al. Integrating transcriptomics and metabolomics to characterise the response of Astragalus membranaceus Bge. var. mongolicus (Bge.) to progressive drought stress[J]. BMC Genomics, 2016, 17(1):88.
[37]	Guldbrandsen N, Kostidis S, Schäfer H,et al. NMR-based metabolomic study on isatis tinctoria:comparison of different accessions, harvesting dates, and the effect of repeated harvesting[J]. J Nat Prod, 2015, 78(5):977-986.
[38]	Goossens A. It is easy to get huge candidate gene lists for plant metabolism now, but how to get beyond?[J]. Mol Plant, 2015, 8(1):2-5.
[39]	Tian L, Hu Y, Chen XY. Advancing human health through exploration of plant metabolism and reaping the benefits of edible medicinal plants[J]. Mol Plant, 2017, 10(3):533-536.
[40]	Wurtzel ET, Kutchan TM. Plant metabolism, the diverse chemistry set of the future[J]. Science, 2016, 353(6305):1232-1236.

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Application in medicinal plants research by high-throughput metabolomics method

doi: 10.3969/j.issn.1006-0111.2017.06.005

Abstract

References

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通讯作者: 陈斌, bchen63@163.com

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