Phytochemical genomics — a new trend
Tài liệu tham khảo
Afendi, 2012, KNApSAcK family databases: integrated metabolite–plant species databases for multifaceted plant research, Plant Cell Physiol, 53, e1, 10.1093/pcp/pcr165
Yonekura-Sakakibara, 2009, Functional genomics for plant natural product biosynthesis, Nat Prod Rep, 26, 1466, 10.1039/b817077k
Saito, 2010, Metabolomics for functional genomics, systems biology, and biotechnology, Annu Rev Plant Biol, 61, 463, 10.1146/annurev.arplant.043008.092035
Neumann, 2010, Computational mass spectrometry for metabolomics: identification of metabolites and small molecules, Anal Bioanal Chem, 398, 2779, 10.1007/s00216-010-4142-5
Horai, 2010, MassBank: a public repository for sharing mass spectral data for life sciences, J Mass Spectrom, 45, 703, 10.1002/jms.1777
Sawada, 2012, RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database, Phytochemistry, 82, 38, 10.1016/j.phytochem.2012.07.007
Udayakumar, 2012, PMDB: Plant Metabolome Database—a metabolomic approach, Med Chem Res, 21, 47, 10.1007/s00044-010-9506-z
Wolf, 2010, In silico fragmentation for computer assisted identification of metabolite mass spectra, BMC Bioinformatics, 11, 148, 10.1186/1471-2105-11-148
Chikayama, 2010, Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum, Anal Chem, 82, 1653, 10.1021/ac9022023
Giavalisco, 2011, Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry, Plant J, 68, 364, 10.1111/j.1365-313X.2011.04682.x
Nakabayashi, 2013, Combination of liquid chromatography-Fourier transform-ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of S-containing metabolites in onion bulbs, Anal Chem, 85, 1310, 10.1021/ac302733c
Sawada, 2009, Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants, Plant Cell Physiol, 50, 37, 10.1093/pcp/pcn183
Watanabe, 2008, Physiological roles of the β-substituted alanine synthase gene family in Arabidopsis, Plant Physiol, 146, 310, 10.1104/pp.107.106831
Redestig, 2010, Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis, BMC Bioinformatics, 11, 214, 10.1186/1471-2105-11-214
Kusano, 2011, Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment, PLoS One, 6, e16989, 10.1371/journal.pone.0016989
Oikawa, 2012, Metabolite analyses of single cells, Plant J, 70, 30, 10.1111/j.1365-313X.2012.04967.x
Tohge, 2011, Toward the storage metabolome: profiling the barley vacuole, Plant Physiol, 157, 1469, 10.1104/pp.111.185710
Oikawa, 2011, Metabolomics of a single vacuole reveals metabolic dynamism in an alga Chara australis, Plant Physiol, 157, 544, 10.1104/pp.111.183772
Korte, 2012, Mass spectrometric imaging as a high-spatial resolution tool for functional genomics: tissue-specific gene expression of TT7 inferred from heterogeneous distribution of metabolites in Arabidopsis flowers, Anal Method, 4, 474, 10.1039/C2AY05618F
Bino, 2004, Potential of metabolomics as a functional genomics tool, Trends Plant Sci, 9, 418, 10.1016/j.tplants.2004.07.004
Matsuda, 2010, AtMetExpress development: a phytochemical atlas of Arabidopsis development, Plant Physiol, 152, 566, 10.1104/pp.109.148031
Bais, 2012, Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics—database and tools update, Nucleic Acids Res, 40, D1216, 10.1093/nar/gkr969
Quanbeck, 2012, Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”, Front Plant Sci, 3, 15, 10.3389/fpls.2012.00015
Matsuda, 2009, MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites, Plant J, 57, 555, 10.1111/j.1365-313X.2008.03705.x
Matsuda, 2011, Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity, Front Plant Sci, 2, 40, 10.3389/fpls.2011.00040
Goda, 2008, The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access, Plant J, 55, 526, 10.1111/j.1365-313X.2008.03510.x
Sakurai, 2013, PRIMe update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation, Plant Cell Physiol, 54, e5, 10.1093/pcp/pcs184
Saito, 2013, The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity, Plant Physiol Biochem, 10.1016/j.plaphy.2013.02.001
Yonekura-Sakakibara, 2008, Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene–metabolite correlations in Arabidopsis, Plant Cell, 20, 2160, 10.1105/tpc.108.058040
Yonekura-Sakakibara, 2012, Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana, Plant J, 69, 154, 10.1111/j.1365-313X.2011.04779.x
Miyahara, 2013, Acyl-glucose-dependent glucosyltransferase catalyzes the final step of anthocyanin formation in Arabidopsis, J Plant Physiol, 10.1016/j.jplph.2012.12.001
Kitamura, 2010, Metabolic profiling and cytological analysis of proanthocyanidins in immature seeds of Arabidopsis thaliana flavonoid accumulation mutants, Plant J, 62, 549, 10.1111/j.1365-313X.2010.04174.x
Stracke, 2010, Analysis of production of flavonol glycosides-dependent flavonol glycoside accumulation in Arabidopsis thaliana plants reveals MYB11-MYB12- and MYB111-independent flavonol glycoside accumulation, New Phytol, 188, 985, 10.1111/j.1469-8137.2010.03421.x
Dubos, 2010, MYB transcription factors in Arabidopsis, Trends Plant Sci, 15, 573, 10.1016/j.tplants.2010.06.005
Sønderby, 2010, Biosynthesis of glucosinolates—gene discovery and beyond, Trends Plant Sci, 15, 283, 10.1016/j.tplants.2010.02.005
de Kraker, 2011, From amino acid to glucosinolate biosynthesis: protein sequence changes in the evolution of methylthioalkylmalate synthase in Arabidopsis, Plant Cell, 23, 38, 10.1105/tpc.110.079269
Sawada, 2009, Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis, Plant Cell Physiol, 50, 1579, 10.1093/pcp/pcp110
Hirai, 2007, Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis, Proc Natl Acad Sci U S A, 104, 6478, 10.1073/pnas.0611629104
Maruyama-Nakashita, 2006, Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism, Plant Cell, 18, 3235, 10.1105/tpc.106.046458
Mugford, 2009, Disruption of adenosine-5-phosphosulfate kinase in Arabidopsis reduces levels of sulfated secondary metabolites, Plant Cell, 21, 910, 10.1105/tpc.109.065581
Geu-Flores, 2011, Cytosolic γ-glutamyl peptidases process glutathione conjugates in the biosynthesis of glucosinolates and camalexin in Arabidopsis, Plant Cell, 23, 2456, 10.1105/tpc.111.083998
Chan, 2011, Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana, PLoS Biol, 9, e1001125, 10.1371/journal.pbio.1001125
Nour-Eldin, 2012, NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds, Nature, 488, 531, 10.1038/nature11285
Kusano, 2011, Metabolomic approaches toward understanding nitrogen metabolism in plants, J Exp Bot, 62, 1439, 10.1093/jxb/erq417
Ward, 2011, Metabolomic analysis of Arabidopsis reveals hemiterpenoid glycosides as products of a nitrate ion-regulated, carbon flux overflow, Proc Natl Acad Sci U S A, 108, 10762, 10.1073/pnas.1018875108
Okazaki, 2013, A new class of plant lipid is essential for protection against phosphorus depletion, Nat Commun, 4, 1510, 10.1038/ncomms2512
Okazaki, 2009, A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis, Plant Cell, 21, 892, 10.1105/tpc.108.063925
Maruyama, 2009, Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A, Plant Physiol, 150, 1972, 10.1104/pp.109.135327
Kusano, 2011, Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light, Plant J, 67, 354, 10.1111/j.1365-313X.2011.04599.x
Fu, 2009, System-wide molecular evidence for phenotypic buffering in Arabidopsis, Nat Genet, 41, 166, 10.1038/ng.308
Routaboul, 2012, Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis, J Exp Bot, 63, 3749, 10.1093/jxb/ers067
Meyer, 2012, Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids, Plant J, 71, 669, 10.1111/j.1365-313X.2012.05021.x
Sulpice, 2010, Network analysis of enzyme activities and metabolite levels and their relationship to biomass in a large panel of Arabidopsis accessions, Plant Cell, 22, 2872, 10.1105/tpc.110.076653
Carreno-Quintero, 2013, Genetic analysis of metabolome–phenotype interactions: from model to crop species, Trends Genet, 29, 41, 10.1016/j.tig.2012.09.006
Albinsky, 2010, Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism, Mol Plant, 3, 125, 10.1093/mp/ssp069
Kusano, 2011, Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice, Plant J, 66, 456, 10.1111/j.1365-313X.2011.04506.x
Matsuda, 2012, Dissection of genotype–phenotype associations in rice grains using metabolome quantitative trait loci analysis, Plant J, 70, 624, 10.1111/j.1365-313X.2012.04903.x
Redestig, 2011, Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics, BMC Syst Biol, 5, 176, 10.1186/1752-0509-5-176
Calingacion, 2012, A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties, Metabolomics, 8, 771, 10.1007/s11306-011-0374-4
Bowne, 2012, Drought responses of leaf tissues from wheat cultivars of differing drought tolerance at the metabolite level, Mol Plant, 5, 418, 10.1093/mp/ssr114
Amiour, 2012, The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize, J Exp Bot, 63, 5017, 10.1093/jxb/ers186
Casati, 2011, Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize, BMC Genomics, 12, 321, 10.1186/1471-2164-12-321
de Vos, 2011, Metabolomics of a model fruit: tomato, vol. 43, 109
Schilmiller, 2009, Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate, Proc Natl Acad Sci U S A, 106, 10865, 10.1073/pnas.0904113106
Schilmiller, 2012, Identification of a BAHD acetyltransferase that produces protective acyl sugars in tomato trichomes, Proc Natl Acad Sci U S A, 109, 16377, 10.1073/pnas.1207906109
Sayama, 2012, The Sg-1 glycosyltransferase locus regulates structural diversity of triterpenoid saponins of soybean, Plant Cell, 24, 2123, 10.1105/tpc.111.095174
Naoumkina, 2010, Genomic and coexpression analyses predict multiple genes involved in triterpene saponin biosynthesis in Medicago truncatula, Plant Cell, 22, 850, 10.1105/tpc.109.073270
Zhao, 2011, MATE2 mediates vacuolar sequestration of flavonoid glycosides and glycoside malonates in Medicago truncatula, Plant Cell, 23, 1536, 10.1105/tpc.110.080804
Augustin, 2012, UDP-glycosyltransferases from the UGT73C subfamily in Barbarea vulgaris catalyze sapogenin 3-O-glucosylation in saponin-mediated insect resistance, Plant Physiol, 160, 1881, 10.1104/pp.112.202747
Yonekura-Sakakibara, 2012, Transcriptome data modeling for targeted plant metabolic engineering, Curr Opin Biotechnol
Giddings, 2011, A stereoselective hydroxylation step of alkaloid biosynthesis by a unique cytochrome P450 in Catharanthus roseus, J Biol Chem, 286, 16751, 10.1074/jbc.M111.225383
Geu-Flores, 2012, An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis, Nature, 492, 138, 10.1038/nature11692
Wurtele, 2012, Medicinal plants: a public resource for metabolomics and hypothesis development, Metabolites, 2, 1031, 10.3390/metabo2041031
Seki, 2011, Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin, Plant Cell, 23, 4112, 10.1105/tpc.110.082685
Bunsupa, 2012, Lysine decarboxylase catalyzes the first step of quinolizidine alkaloid biosynthesis and coevolved with alkaloid production in Leguminosae, Plant Cell, 24, 1202, 10.1105/tpc.112.095885
Asano, 2012, Suppression of camptothecin biosynthetic genes results in metabolic modification of secondary products in hairy roots of Ophiorrhiza pumila, Phytochemistry
Yamazaki, 2013, 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, Plant Cell Physiol, 10.1093/pcp/pct040
Gagne, 2012, Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides, Proc Natl Acad Sci U S A, 109, 12811, 10.1073/pnas.1200330109
Stout, 2012, The hexanoyl-CoA precursor for cannabinoid biosynthesis is formed by an acyl-activating enzyme in Cannabis sativa trichomes, Plant J, 71, 353
Gesell, 2009, CYP719B1 is salutaridine synthase, the C-C phenol-coupling enzyme of morphine biosynthesis in opium poppy, J Biol Chem, 284, 24432, 10.1074/jbc.M109.033373
Hagel, 2010, Dioxygenases catalyze the O-demethylation steps of morphine biosynthesis in opium poppy, Nat Chem Biol, 6, 273, 10.1038/nchembio.317
Winzer, 2012, A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine, Science, 336, 1704, 10.1126/science.1220757
Fukushima, 2009, Integrated omics approaches in plant systems biology, Curr Opin Chem Biol, 13, 532, 10.1016/j.cbpa.2009.09.022
Field, 2011, Formation of plant metabolic gene clusters within dynamic chromosomal regions, Proc Natl Acad Sci U S A, 108, 16116, 10.1073/pnas.1109273108
Sirikantaramas, 2008, Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants, Proc Natl Acad Sci U S A, 105, 6782, 10.1073/pnas.0801038105
van Bakel, 2011, The draft genome and transcriptome of Cannabis sativa, Genome Biol, 12, R102, 10.1186/gb-2011-12-10-r102