Genomics Grand for Diversified Plant Secondary Metabolites

doi:10.3724/SP.J.1143.2011.10233

Abstract

Abstract:

Plants can generate an overwhelming variety of structurally diversified organic compounds called secondary metabolites. These compounds usually perform interesting biological activities and important functions in influencing interactions between plants and other organisms. They are also widely utilized as pharmaceuticals, insecticides, dyes, flavors and fragrances. Plant genome sequencing, transcriptome and metabolome analyses have provided huge amounts of data to explain the great diversity of secondary metabolites. This knowledge in turn will help us better understand their ecological role and is a creating novel tool for genetic engineering of plant secondary metabolism.

Key words: Plant secondary metabolites, Biosynthetic pathways, Genomics, Chemical diversity, Bioinformatics

摘要：

关键词: Plant secondary metabolites, Biosynthetic pathways, Genomics, Chemical diversity, Bioinformatics

CLC Number:

Q 946.8

Xin FANG, Chang-Qing YANG, Yu-Kun WEI, Qi-Xia MA, Lei YANG, Xiao-Ya CHEN . Genomics Grand for Diversified Plant Secondary Metabolites[J]. Plant Diversity, 2011, 33(01): 53-64.

Xin FANG1、2, Chang-Qing YANG2, Yu-Kun WEI1, Qi-Xia MA1, Lei YANG1、2, Xiao-. Genomics Grand for Diversified Plant Secondary Metabolites[J]. Plant Diversity, 2011, 33(01): 53-64.

References

Aubourg S, Lecharny A, Bohlmann J, 2002. Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana ［J］. Molecular Genetics & Genomics, 267: 730—745
Ayabe SI, Akashi T, 2006. Cytochrome P450s in flavonoid metabolism［J］. Phytochemistry Reviews , 5: 271—282
Bouwmeester HJ, Wallaart TE, Janssen MHA et al., 1999. Amorpha-4,11-diene synthase catalyses the first probable step in artemisinin biosynthesis［J］. Phytochemistry, 52: 843—854
Buchanan BB, Gruissem W, Jones RL, 2000. Biochemistry and Molecular Biology of Plants［M］. Rockville: American Society of Plant Physiologists
Cai Y, Jia JW, Crock J et al., 2002. A cDNA clone for β-caryophyllene synthase from Artemisia annua［J］. Phytochemistry, 61: 523—529
Chen F, Liu CJ, Tschaplinske TJ et al., 2009. Genomics of secondary metabolism in Populus: interactions with biotic and abiotic environments［J］. Critical Reviews in Plant Sciences, 28: 375—392
Chung H, Sztal T, Pasricha S et al., 2008. Characterization of Drosophila melanogaster cytochrome P450 genes［J］. Proceedings of the National Academy of Sciences of the United States of America, 106: 5731—5736
Connolly JD, Hill RA, 2010. Triterpenoids［J］. Natural Product Reports, 27: 79—132
D′Auria JC, 2006. Acyltransferases in plants: a good time to be BAHD［J］. Current Opinion in Plant Biology, 9: 331—340
Davies KM, Schwinn KE, 2003. Transcriptional regulation of secondary metabolism［J］. Functional Plant Biology, 30: 913—925.
Davin LB, Wang HB, Crowell AL et al., 1997. Stereoselective bimolecular phenoxy tadical coupling by an auxiliary (dirigent) protein without an active center［J］. Science, 275: 362—366
DellaPenna D, Last RL, 2008. Genome-enabled approaches shed new light on plant metabolism［J］. Science, 320: 479—481
Dewick PM, 2002. Medicinal Natural Products［M］. Baffins lane: John Wiley & Sons Ltd
Dey PM, Harborne JB, 1997. Plant Biochemistry［M］. San Diego: Academic Press Ltd
Dudareva N, Andersson S, Orlova I et al., 2005. The nonmevalonate pathway supports both monterpene and sesquiterpene formation in snapdragon flowers［J］. Proceedings of the National Academy of Sciences of the United States of America, 102: 933—938
Dudareva N, Pichersky E, 2000. Biochemical and molecular genetic aspects of floral scents［J］. Plant Physiolosy, 122: 627—633
Espley RV, Brendolise C, Chagné D et al., 2009. Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples［J］. The Plant Cell, 21: 168—183
Fazio GC, Xu R, Matsuda SPT, 2004. Genome mining to identify new plant triterpenoids［J］. Journal of the American Chemical Society, 126: 5678—5679
Field B, Osbourn AE, 2008. Metabolic diversification-independent assembly of operon-like gene clusters in different plants［J］. Science, 320: 543—547
Fischbach MA, Walsh CT, Clardy J, 2008. The evolution of gene collectives: how natural selection drives chemical innovation［J］. Proceedings of the National Academy of Sciences of the United States of America, 105: 4601—4608
Firn RD, Jones CG, 2003. Natural products-a simple model to explain chemical diversity［J］. Natural Product Reports, 20: 382—391
Finkle BJ, Nelson RF, 1963. Enzyme reactions with phenolic compounds: a meta-O-methyltransferase in plants［J］. Biochimica et Biophysica Acta, 78: 747—749
Fraga BM, 1997. Natural sesquiterpenoids［J］. Natural Product Reports, 14: 145—162
Gang DR, 2005. Evolution of flavors and scents［J］. Annual Review of Plant Biology, 56: 301—325
GierlA, Frey M, 2001. Evolution of benzoxazinone biosynthesis and indole production in maize［J］. Planta, 213: 493—498
Grayson DH, 2000. Monoterpenoids［J］. Natural Product Reports, 17: 385—419
Hanson JR, 2004. Diterpenoids［J］. Natural Product Reports, 21: 785—793
Holton TA, Cornish EC, 1989. Genetics and biochemistry of anthocyanin biosynthesis［J］. The Plant Cell, 7: 1071—1083
Jia JW, Crock J, Lu S et al., 1999. (3R)-Linalool synthase from Artemisia annua L.: cDNA isolation, characterization, and wound induction［J］. Archives of Biochemistry and Biophysics, 372: 143—149
Koukol J, Conn EE, 1961. The metabolism of aromatic compounds in higher plant: purification and properties of the phenylalanine deaminase of Hordeum vulgare［J］. The Journal of Biological Chemistry, 236: 2692—2698
Lichtenthaler HK, 1999. The 1-deoxy-D-xylulose-5-phosphate pathway of isoprenoid biosynthesis in plants［J］. Annual Review of Plant Physiology and Plant Molecular Biology, 50: 47—65
Lu S, Xu R, Jia JW et al., 2002. Cloning and functional characterization of a β-pinene synthase from Artemisia annua that shows a circadian pattern of expression［J］. Plant Physiolosy, 130: 477—486
Luo J, Fuell C, Parr A et al., 2009. A novel polyamine acyltransferase responsible for the accumulation of spermidine conjugates in Arabidopsis seed［J］. The Plant Cell, 21: 318—333
Luo P, Wang YH, Wang GD et al., 2001. Molecular cloning and functional identification of (+)-d-cadinene-8-hydroxylase, a cytochrome P450 monooxygenase (CYP706B1) of cotton sesquiterpene biosynthesis［J］. The Plant Journal, 28: 95—104
Menzel R, Bogaert T, Achazi R, 2001. Asystematic gene expression screen of Caenorhabditis elegans cytochrome P450 genes reveals CYP35 as strongly Xenobiotic inducible［J］. Archives of Biochemistry and Biophysics, 395: 158—168
Mizutani M, Ohta D, 2010. Diversification of P450 genes during land plant evolution［J］. Annual Review of Plant Biology, 61: 1—25
Neish AC, 1961. Formation of m- and p-coumaric acids by enzymatic deamination of the corresponding isomers of tyrosine［J］. Phytochemistry, 1: 1—24
Nelson DR, Zeldin DC, Hoffman SMG et al., 2004. Comparison of cytochrome P450 (CYP) genes from mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternativesplice variants［J］. Pharmacogenetics and Genomics, 14: 1—18
Newman JD, Chappell J, 1999. Isoprenoid biosynthesis in plants: carbon partitioning within the cytoplasmic pathway［J］. Critical Reviews in Biochemistry and Molecular Biology, 34: 95—106
Ohishi Y, Ishikawa J, Hara H et al., 2008. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350［J］. The Journal of Bacteriology, 190: 4050—4060
mura S, Ikeda H, Ishikawa J et al., 2001. Genome sequence of an industrial microoganism Streptomyces avermitilis deducing the ability of producing secondary metabolites［J］. Proceedings of the National Academy of Sciences of the United States of America, 98: 12215—12220
Picaud S, Olofsson L, Brodelius M et al., 2005. Expression, purification, and characterization of recombinant amorpha-4,11-diene synthase from Artemisia annua L.［J］. Archives of Biochemistry and Biophysics, 436: 215—226
Russell DW, Conn EE, 1967. The cinnamic acid 4-hydraxylase of pea seedlings［J］. Archives of Biochemistry and Biophysics, 122: 256—258
Shimura K, Okada A, Okada K et al., 2007. Identification of a biosynthetic gene cluster in rice for momilactones［J］. The Journal of Biological Chemistry, 282: 34013—34018
Swaminathan S, Morrone D, Wang Q et al., 2009. CYP76M7 is an ent-Cassadiene C11α-Hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice［J］. The Plant Cell, 21: 3315—3325
Trethewey RN, 2004. Metabolite profiling as an aid to metabolic engineering in plants［J］. Current Opinion in Plant Biology, 7: 196—201
Wallaart TE, Bouwmeester HJ, Hille J et al., 2001. Amorpha-4,11-diene synthase: cloning and functional expression of a key enzyme in the biosynthetic pathway of the novel antimalarial drug artemisinin［J］. Planta, 212: 460—465
Walsh CT, Fischabch MA, 2010. Natural products version 2.0: connecting genes to molecules［J］. Journal of the American Chemical Society, 132: 2469—2493
Yu XH, Gou JY, Liu CJ, 2009. BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: bioinformatics and gene expression［J］. Plant Molecular Biology, 70: 421—442
Yu XH, Chen MH, Liu CJ, 2008. Nucleocytoplasmic-localized acyltransferases catalyze the malonylation of 7-O-glycosidic (iso)flavones in Medicago truncatula［J］. The Plant Journal, 55: 382—396
Ziegler J, Facchini PJ, 2008. Alkaloid biosynthesis: metabolism and trafficking［J］. Annual Review of Plant Biology, 59: 735—769

[1]	Na-Na Zhang (张娜娜), Gregory W. Stull, Xue-Jie Zhang (张学杰), Shou-Jin Fan (樊守金), Ting-Shuang Yi (伊廷双), Xiao-Jian Qu (曲小健). PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics [J]. Plant Diversity, 2025, 47(04): 544-560.
[2]	Zhi-Qiong Mo (莫智琼), Chao-Nan Fu (付超男), Alex D. Twyford, Pete M. Hollingsworth, Ting Zhang (张挺), Jun-Bo Yang (杨俊波), De-Zhu Li (李德铢), Lian-Ming Gao (高连明). Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron [J]. Plant Diversity, 2025, 47(04): 593-603.
[3]	Lang Li (李朗), Bing Liu (刘冰), Yu Song (宋钰), Hong-Hu Meng (孟宏虎), Xiu-Qin Ci (慈秀芹), John G. Conran, Rogier P.J. de Kok, Pedro Luís Rodrigues de Moraes, Jun-Wei Ye (叶俊伟), Yun-Hong Tan (谭运洪), Zhi-Fang Liu (刘志芳), Marlien van der Merwe, Henk van der Werff, Yong Yang (杨永), Jens G. Rohwer, Jie Li (李捷). Global advances in phylogeny, taxonomy and biogeography of Lauraceae [J]. Plant Diversity, 2025, 47(03): 341-364.
[4]	Kai Chen, Yan-Chun Liu, Yue Huang, Xu-Kun Wu, Hai-Ying Ma, Hua Peng, De-Zhu Li, Peng-Fei Ma. Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences [J]. Plant Diversity, 2025, 47(03): 382-393.
[5]	Kai-Yun Chen, Jin-Dan Wang, Rui-Qi Xiang, Xue-Dan Yang, Quan-Zheng Yun, Yuan Huang, Hang Sun, Jia-Hui Chen. Backbone phylogeny of Salix based on genome skimming data [J]. Plant Diversity, 2025, 47(02): 178-188.
[6]	Gulbar Yisilam, Enting Zheng, Chuanning Li, Zhiyong Zhang, Ying Su, Zhenzhou Chu, Pan Li, Xinmin Tian. The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance [J]. Plant Diversity, 2025, 47(02): 201-213.
[7]	Amos Kipkoech, Ke Li, Richard I. Milne, Oyetola Olusegun Oyebanji, Moses C. Wambulwa, Xiao-Gang Fu, Dennis A. Wakhungu, Zeng-Yuan Wu, Jie Liu. An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae) [J]. Plant Diversity, 2025, 47(02): 229-243.
[8]	Yongli Wang, Yan-Da Li, Shuo Wang, Erik Tihelka, Michael S. Engel, Chenyang Cai. Modeling compositional heterogeneity resolves deep phylogeny of flowering plants [J]. Plant Diversity, 2025, 47(01): 13-20.
[9]	Liansheng Xu, Zhuqiu Song, Tian Li, Zichao Jin, Buyun Zhang, Siyi Du, Shuyuan Liao, Xingjie Zhong, Yousheng Chen. New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq) [J]. Plant Diversity, 2025, 47(01): 21-33.
[10]	Zheng-Yu Zuo, Germinal Rouhan, Shi-Yong Dong, Hong-Mei Liu, Xin-Yu Du, Li-Bing Zhang, Jin-Mei Lu. A revised classification of Dryopteridaceae based on plastome phylogenomics and morphological evidence, with the description of a new genus, Pseudarachniodes [J]. Plant Diversity, 2025, 47(01): 34-52.
[11]	Tian-Rui Wang, Xin Ning, Si-Si Zheng, Yu Li, Zi-Jia Lu, Hong-Hu Meng, Bin-Jie Ge, Gregor Kozlowski, Meng-Xiao Yan, Yi-Gang Song. Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species [J]. Plant Diversity, 2025, 47(01): 53-67.
[12]	Yiqing Chen, Lina Dong, Huiqin Yi, Catherine Kidner, Ming Kang. Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts [J]. Plant Diversity, 2024, 46(05): 575-584.
[13]	Xiang-Zhou Hu, Cen Guo, Sheng-Yuan Qin, De-Zhu Li, Zhen-Hua Guo. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae) [J]. Plant Diversity, 2024, 46(03): 344-352.
[14]	Zhen Yang, Lisong Liang, Weibo Xiang, Lujun Wang, Qinghua Ma, Zhaoshan Wang. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis [J]. Plant Diversity, 2024, 46(03): 294-308.
[15]	Yumeng Ren, Lushui Zhang, Xuchen Yang, Hao Lin, Yupeng Sang, Landi Feng, Jianquan Liu, Minghui Kang. Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing [J]. Plant Diversity, 2024, 46(02): 169-180.