Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plantLonicera japonica thunb

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• 作者：Yuan Yuan (1)
  Lipu Song (2)
  Minhui Li (1) (4)
  Guiming Liu (2)
  Yanan Chu (2)
  Luyu Ma (3)
  Yuanyuan Zhou (2)
  Xiao Wang (1) (5)
  Wei Gao (1)
  Shuangshuang Qin (1)
  Jun Yu (2)
  Xumin Wang (2)
  Luqi Huang (1)
  
• 关键词：RNA ; seq ; Transcriptome ; Active compounds ; Synthetic pathways ; Flos Lonicerae Japonicae
• 刊名：BMC Genomics
• 出版年：2012
• 出版时间：December 2012
• 年：2012
• 卷：13
• 期：1
• 全文大小：943KB
• 参考文献：1. Hong SZJ, Yang G, Luo X: Earliest report of Flos Lonicerae Japonicae and its medical organ. / Zhongyaocai 1997, 20:2.
  2. Xiang T, Xiong QB, Ketut AI, Tezuka Y, Nagaoka T, Wu LJ, Kadota S: Studies on the hepatocyte protective activity and the structure-activity relationships of quinic acid and caffeic acid derivatives from the flower buds of Lonicera bournei. / Planta Med 2001, 67:322鈥?25. CrossRef
  3. Yoo HJ, Kang HJ, Song YS, Park EH, Lim CJ: Anti-angiogenic, antinociceptive and anti-inflammatory activities of Lonicera japonica extract. / J Pharm Pharmacol 2008, 60:779鈥?86. CrossRef
  4. Hsu SL, Chen CY, Peng WH, Wu LC, Wu CC: Luteolin Ameliorates Experimental Lung Fibrosis Both in Vivo and in Vitro: Implications for Therapy of Lung Fibrosis. / J Agr Food Chem 2010, 58:11653鈥?1661. CrossRef
  5. Li P, Qi LW, Chen CY: Structural characterization and identification of iridoid glycosides, saponins, phenolic acids and flavonoids in Flos Lonicerae Japonicae by a fast liquid chromatography method with diode-array detection and time-of-flight mass spectrometry. / Rapid Commun Mass Sp 2009, 23:3227鈥?242. CrossRef
  6. Chung JH, Ryu KH, Rhee HI, Kim JH, Yoo H, Lee BY, Um KA, Kim K, Noh JY, Lim KM: Anti-Inflammatory and Analgesic Activities of SKLJI, a Highly Purified and Injectable Herbal Extract of Lonicera japonica. / Biosci Biotech Bioch 2010, 74:2022鈥?028. CrossRef
  7. Chang KC, Jeong JJ, Ha YM, Jin YC, Lee EJ, Kim JS, Kim HJ, Seo HG, Lee JH, Kang SS, / et al.: Rutin from Lonicera japonica inhibits myocardial ischemia/reperfusion-induced apoptosis in vivo and protects H9c2 cells against hydrogen peroxide-mediated injury via ERK1/2 and PI3K/Akt signals in vitro. / Food Chem Toxicol 2009, 47:1569鈥?576. CrossRef
  8. Ge B, LX, Yi K, Tian Y: The Active Constituent and Pharmaceutical Action of Flos Lonicerae and Its Application. / Chinese Wild Plant Resources 2004, 23:5.
  9. El-Sayed AM, Mitchell VJ, McLaren GF, Manning LM, Bunn B, Suckling DM: Attraction of New Zealand Flower Thrips, Thrips obscuratus, to cis-Jasmone, a Volatile Identified from Japanese Honeysuckle Flowers. / J Chem Ecol 2009, 35:656鈥?63. CrossRef
  10. Geng S, Ning X, Wu H, Lin H, Zhao S, Xu H: The Structure of Flower in Different Developmental Stages in Relation to the Varieties of Chlorogenic Acid Content in Lonicera confusa. / Acta Botanica Yunnanica 2005,27(3):279鈥?87.
  11. Bai GB, Peng XX, Li WD, Wang WQ: Cloning and Characterization of a cDNA Coding a Hydroxycinnamoyl-CoA Quinate Hydroxycinnamoyl Transferase Involved in Chlorogenic Acid Biosynthesis in Lonicera japonica. / Planta Med 2010, 76:1921鈥?926. CrossRef
  12. Jiang K, Pi Y, Huang Z, Hou R, Zhang Z, Lin J, Sun X, Tang K: Molecular cloning and mRNA expression profiling of the first specific jasmonate biosynthetic pathway gene allene oxide synthase from Hyoscyamus niger. / Russ J Genet 2009, 45:430鈥?39. CrossRef
  13. Yang M, HF, Zhang L: Comparison on the Chlorogenic Acid Contents in Different Kinds and Different Parts of Flos Lonicerae. / Journal of Instrumental Analysis 2006, 25:122鈥?23.
  14. HC (Ed): / Lonicerae Japonicae. Science Press, Beijing; 1998.
  15. Qin S, YY, Hu G, Chen X, Li X: Comparison of active compounds between Lonicera japonica Thunb and their variation. / China J of Exper Tran Med Form 2010, 16:2.
  16. Lei Z, ZR, Zeng R, He Y: Comparative experiments on antipyretic effect between Lonicera macrathodes Hands Mazz. and the certified Flos Lonicera. / Journal of Hunan Traditional Chinese Medicine University of Hunan 2005, 5:2.
  17. Bahler J, Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J: Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. / Nature 2008, 453:U1239-U1239. CrossRef
  18. Snyder M, Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M: The transcriptional landscape of the yeast genome defined by RNA sequencing. / Science 2008, 320:1344鈥?349. CrossRef
  19. Wold B, Mortazavi A, Williams BA, Mccue K, Schaeffer L: Mapping and quantifying mammalian transcriptomes by RNA-Seq. / Nat Methods 2008, 5:621鈥?28. CrossRef
  20. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I: ABySS: a parallel assembler for short read sequence data. / Genome Res 2009, 19:1117鈥?123. CrossRef
  21. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. / Nucleic Acids Res 1997, 25:3389鈥?402. CrossRef
  22. Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. / Nucleic Acids Res 2000, 28:27鈥?0. CrossRef
  23. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, / et al.: The COG database: an updated version includes eukaryotes. / BMC Bioinforma 2003, 4:41. CrossRef
  24. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, / et al.: InterPro: the integrative protein signature database. / Nucleic Acids Res 2009, 37:D211-D215. CrossRef
  25. Aparicio G, Gotz S, Conesa A, Segrelles D, Blanquer I, Garcia JM, Hernandez V, Robles M, Talon M: Blast2GO goes Grid: Developing a Grid-Enabled Prototype for Functional Genomics Analysis. / St Heal T 2006, 120:194鈥?04.
  26. Maere S, Heymans K, Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. / Bioinformatics 2005, 21:3448鈥?449. CrossRef
  27. Li R, Li Y, Kristiansen K, Wang J: SOAP: Short oligonucleotide alignment program. / Bioinformatics 2008, 24:713鈥?14. CrossRef
  28. Dewey CN, Li B, Ruotti V, Stewart RM, Thomson JA: RNA-Seq gene expression estimation with read mapping uncertainty. / Bioinformatics 2010, 26:493鈥?00. CrossRef
  29. Harris RS: / Improved pairwise alignment of genomic DNA. Ph. D. Thesis. The Pennsylvania State University, ; 2007.
  30. Wang XW, Wang LK, Feng ZX, Wang X, Zhang XG: DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. / Bioinformatics 2010, 26:136鈥?38. CrossRef
  31. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer ELL: The Pfam protein families database. / Nucleic Acids Res 2000, 28:263鈥?66. CrossRef
  32. Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. / Science 1997, 278:631鈥?37. CrossRef
  33. Cameron M, Williams HE, Cannane A: Improved gapped alignment in BLAST. / Ieee Acm T Comput Bi 2004, 1:116鈥?29.
  34. Munoz-Bertomeu J, Cascales-Minana B, Alaiz M, Segura J, Ros R: A critical role of plastidial glycolytic glyceraldehyde-3-phosphate dehydrogenase in the control of plant metabolism and development. / Plant Signal Behav 2010,5(1):67鈥?9. CrossRef
  35. Munoz-Bertomeu J, Cascales-Minana B, Mulet JM, Baroja-Fernandez E, Pozueta-Romero J, Kuhn JM, Segura J, Ros R: Plastidial glyceraldehyde-3-phosphate dehydrogenase deficiency leads to altered root development and affects the sugar and amino acid balance in Arabidopsis. / Plant Physiol 2009, 151:541鈥?58. CrossRef
  36. Lee Y, Choi H, Jin JY, Choi S, Hwang JU, Kim YY, Suh MC: An ABCG/WBC-type ABC transporter is essential for transport of sporopollenin precursors for exine formation in developing pollen. / Plant J 2011, 65:181鈥?93. CrossRef
  37. Jiang LW, Wang H, Tse YC, Law AHY, Sun SSM, Sun YB, Xu ZF, Hillmer S, Robinson DG: Vacuolar sorting receptors (VSRs) and secretory carrier membrane proteins (SCAMPs) are essential for pollen tube growth. / Plant J 2010, 61:826鈥?38. CrossRef
  38. Mellema S, Eichenberger W, Rawyler A, Suter M, Tadege M, Kuhlemeier C: The ethanolic fermentation pathway supports respiration and lipid biosynthesis in tobacco pollen. / Plant J 2002, 30:329鈥?36. CrossRef
  39. Rodriguez-Concepcion M, Fores O, Martinez-Garcia JF, Gonzalez V, Phillips MA, Ferrer A, Boronat A: Distinct light-mediated pathways regulate the biosynthesis and exchange of isoprenoid precursors during Arabidopsis seedling development. / Plant Cell 2004, 16:144鈥?56. CrossRef
  40. Ha SH, Kim JB, Hwang YS, Lee SW: Molecular characterization of three 3-hydroxy-3-methylglutaryl-CoA reductase genes including pathogen-induced Hmg2 from pepper (Capsicum annuum). / Bba-Gene Struct Expr 2003, 1625:253鈥?60. CrossRef
  41. Chappell J, Vonlanken C, Vogeli U: Elicitor-Inducible 3-Hydroxy-3-Methylglutaryl Coenzyme-a Reductase-Activity Is Required for Sesquiterpene Accumulation in Tobacco Cell-Suspension Cultures. / Plant Physiol 1991, 97:693鈥?98. CrossRef
  42. Arimura G, Huber DP, Bohlmann J: Forest tent caterpillars (Malacosoma disstria) induce local and systemic diurnal emissions of terpenoid volatiles in hybrid poplar (Populus trichocarpa x deltoides): cDNA cloning, functional characterization, and patterns of gene expression of (鈭?-germacrene D synthase, PtdTPS1. / Plant J 2004, 37:603鈥?16. CrossRef
  43. Zhuang X, Klingeman WE, Hu J, Chen F: Emission of volatile chemicals from flowering dogwood (cornus Florida L.) flowers. / J Agric Food Chem 2008, 56:9570鈥?574. CrossRef
  44. Aharoni A, Galili G: Metabolic engineering of the plant primary-secondary metabolism interface. / Curr Opin Biotechnol 2011, 22:239鈥?44. CrossRef
  45. Givan CV: Evolving concepts in plant glycolysis: two centuries of progress. / Biol Rev 1999, 74:277鈥?09. CrossRef
  46. Hausler RE, Prabhakar V, Lottgert T, Geimer S, Dormann P, Kruger S, Vijayakumar V, Schreiber L, Gobel C, Feussner K, / et al.: Phosphoenolpyruvate Provision to Plastids Is Essential for Gametophyte and Sporophyte Development in Arabidopsis thaliana. / Plant Cell 2010, 22:2594鈥?617. CrossRef
  47. Vanderstraeten D, Rodriguespousada RA, Goodman HM, Vanmontagu M: Plant Enolase - Gene Structure, Expression, and Evolution. / Plant Cell 1991, 3:719鈥?35.
  48. Angelin B, Einarsson K, Liljeqvist L, Nilsell K, Heller RA: 3-Hydroxy-3-Methylglutaryl Coenzyme-a Reductase in Human-Liver Microsomes - Active and Inactive Forms and Cross-Reactivity with Antibody against Rat-Liver Enzyme. / J Lipid Res 1984, 25:1159鈥?166.
  49. Morin RJ, Noble NA, Srikantaiah MV: Modulation of 3-Hydroxy-3-Methyl Glutaryl Coa Reductase by 2,3-Diphosphoglyceric Acid. / Experientia 1984, 40:953鈥?55. CrossRef
  50. Ibsen KH, TP, Basabe J (Eds): / Properties of Rat Pyruvate Kinase Isozymes. Academic Press, Inc, New York; 1975.
  51. Rohde A, Morreel K, Ralph J, Goeminne G, Hostyn V, De Rycke R, Kushnir S, Van Doorsselaere J, Joseleau JP, Vuylsteke M, / et al.: Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. / Plant Cell 2004, 16:2749鈥?771. CrossRef
  52. Matt P, Krapp A, Haake V, Mock HP, Stitt M: Decreased Rubisco activity leads to dramatic changes of nitrate metabolism, amino acid metabolism and the levels of phenylpropanoids and nicotine in tobacco antisense RBCS transformants. / Plant J 2002, 30:663鈥?77. CrossRef
  53. Moriizumi S, Gourdon L, Lefrancois-Martinez AM, Kahn A, Raymondjean M: Effect of different basic helix-loop-helix leucine zipper factors on the glucose response unit of the L-type pyruvate kinase gene. / Gene Expr 1998, 7:103鈥?13.
  54. Ma L, Sham YY, Walters KJ, Towle HC: A critical role for the loop region of the basic helix-loop-helix/leucine zipper protein Mlx in DNA binding and glucose-regulated transcription. / Nucleic Acids Res 2007, 35:35鈥?4. CrossRef
  55. Li MV, Chang B, Imamura M, Poungvarin N, Chan L: Glucose-dependent transcriptional regulation by an evolutionarily conserved glucose-sensing module. / Diabetes 2006, 55:1179鈥?189. CrossRef
  56. Maffi D, Iriti M, Pigni M, Vannini C, Faoro F: Uromyces appendiculatus infection in BTH-treated bean plants: ultrastructural details of a lost fight. / Mycopathologia 2011, 171:209鈥?21. CrossRef
  57. Fukasawa-Akada T, Kung SD, Watson JC: Phenylalanine ammonia-lyase gene structure, expression, and evolution in Nicotiana. / Plant Mol Biol 1996, 30:711鈥?22. CrossRef
  58. Nishihara M, Nakatsuka T, Yamamura S: Flavonoid components and flower color change in transgenic tobacco plants by suppression of chalcone isomerase gene. / FEBS Lett 2005, 579:6074鈥?078. CrossRef
  59. Dobritsa AA, Lei Z, Nishikawa S, Urbanczyk-Wochniak E, Huhman DV, Preuss D, Sumner LW: LAP5 and LAP6 encode anther-specific proteins with similarity to chalcone synthase essential for pollen exine development in Arabidopsis. / Plant Physiol 2010, 153:937鈥?55. CrossRef
  60. Douglas CJ, Souza CD, Kim SS, Koch S, Kienow L, Schneider K, McKim SM, Haughn G, Kombrink E: A Novel Fatty Acyl-CoA Synthetase Is Required for Pollen Development and Sporopollenin Biosynthesis in Arabidopsis. / Plant Cell 2009, 21:507鈥?25. CrossRef
  61. Komatsuda T, Sakuma S, Pourkheirandish M, Matsumoto T, Koba T: Duplication of a well-conserved homeodomain-leucine zipper transcription factor gene in barley generates a copy with more specific functions. / Funct Integr Genomic 2010, 10:123鈥?33. CrossRef
  
• 作者单位：Yuan Yuan (1)
  Lipu Song (2)
  Minhui Li (1) (4)
  Guiming Liu (2)
  Yanan Chu (2)
  Luyu Ma (3)
  Yuanyuan Zhou (2)
  Xiao Wang (1) (5)
  Wei Gao (1)
  Shuangshuang Qin (1)
  Jun Yu (2)
  Xumin Wang (2)
  Luqi Huang (1)
  
  1. Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700, China
  2. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
  4. Baotou Medical College, Baotou, 014040, China
  3. Shandong Academy of Medical Sciences, Jinan, 250031, China
  5. Shandong Analysis and Test center, Jinan, 250014, China
  

文摘

Background Traditional Chinese medicine uses various herbs for the treatment of various diseases for thousands of years and it is now time to assess the characteristics and effectiveness of these medicinal plants based on modern genetic and molecular tools. The herb Flos Lonicerae Japonicae (FLJ or Lonicera japonica Thunb.) is used as an anti-inflammatory agent but the chemical quality of FLJ and its medicinal efficacy has not been consistent. Here, we analyzed the transcriptomes and metabolic pathways to evaluate the active medicinal compounds in FLJ and hope that this approach can be used for a variety of medicinal herbs in the future. Results We assess transcriptomic differences between FLJ and L. japonica Thunb. var. chinensis (Watts) (rFLJ), which may explain the variable medicinal effects. We acquired transcriptomic data (over 100 million reads) from the two herbs, using RNA-seq method and the Illumina GAII platform. The transcriptomic profiles contain over 6,000 expressed sequence tags (ESTs) for each of the three flower development stages from FLJ, as well as comparable amount of ESTs from the rFLJ flower bud. To elucidate enzymatic divergence on biosynthetic pathways between the two varieties, we correlated genes and their expression profiles to known metabolic activities involving the relevant active compounds, including phenolic acids, flavonoids, terpenoids, and fatty acids. We also analyzed the diversification of genes that process the active compounds to distinguish orthologs and paralogs together with the pathways concerning biosynthesis of phenolic acid and its connections with other related pathways. Conclusions Our study provides both an initial description of gene expression profiles in flowers of FLJ and its counterfeit rFLJ and the enzyme pool that can be used to evaluate FLJ quality. Detailed molecular-level analyses allow us to decipher the relationship between metabolic pathways involved in processing active medicinal compounds and gene expressions of their processing enzymes. Our evolutionary analysis revealed specific functional divergence of orthologs and paralogs, which lead to variation in gene functions that govern the profile of active compounds.