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Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the side-chain elongation steps of aliphatic glucosinolate biosynthesis

Amino Acids volume 39, pages 1067–1075 (2010)Cite this article

Abstract

Amino acid and glucosinolate biosynthesis are two interdependent pathways; amino acid synthesis as a part of primary metabolism provides the precursors for glucosinolate biosynthesis in secondary metabolism. In our previous studies, the combination of coexpression analysis and metabolite profiling led to the identification of genes and key regulators involved in glucosinolate biosynthesis. Moreover, the integration of transcriptome and metabolome data of sulphur-deprived Arabidopsis plants revealed coordinate changes in the expression profiles of genes involved in glucosinolate and amino acid metabolism.

This review provides an overview of our recent studies involving Arabidopsis mutant plants that exhibit impairment in the side-chain elongation process occurring during aliphatic glucosinolate biosynthesis by means of coexpression analysis and a novel metabolite profiling approach based on ultra-performance liquid chromatography coupled with tandem quadrupole mass spectrometry (UPLC-TQMS) (Sawada et al. 2009a). Thus, this review highlights the advantages of the omics-based approach in identifying genes involved in glucosinolate biosynthesis.

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References

  • Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48:381–390

    Article  PubMed  CAS  Google Scholar 

  • Bak S, Feyereisen R (2001) The involvement of two p450 enzymes, CYP83B1 and CYP83A1, in auxin homeostasis and glucosinolate biosynthesis. Plant Physiol 127:108–118

    Article  PubMed  CAS  Google Scholar 

  • Bak S, Tax FE, Feldmann KA, Galbraith DW, Feyereisen R (2001) CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell 13:101–111

    Article  PubMed  CAS  Google Scholar 

  • Barlier I, Kowalczyk M, Marchant A, Ljung K, Bhalerao R, Bennett M, Sandberg G, Bellini C (2000) The SUR2 gene of Arabidopsis thaliana encodes the cytochrome P450 CYP83B1, a modulator of auxin homeostasis. Proc Natl Acad Sci USA 97:14819–14824

    Article  PubMed  CAS  Google Scholar 

  • Beekwilder J, van Leeuwen W, van Dam NM, Bertossi M, Grandi V, Mizzi L, Soloviev M, Szabados L, Molthoff JW, Schipper B, Verbocht H, de Vos RC, Morandini P, Aarts MG, Bovy A (2008) The impact of the absence of aliphatic glucosinolates on insect herbivory in Arabidopsis. PLoS One 3:e2068

    Article  PubMed  CAS  Google Scholar 

  • Brown PD, Tokuhisa JG, Reichelt M, Gershenzon J (2003) Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana. Phytochemistry 62:471–481

    Article  PubMed  CAS  Google Scholar 

  • Chen S, Glawischnig E, Jorgensen K, Naur P, Jorgensen B, Olsen CE, Hansen CH, Rasmussen H, Pickett JA, Halkier BA (2003) CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J 33:923–937

    Article  PubMed  CAS  Google Scholar 

  • Cho K, Shibato J, Agrawal GK, Jung YH, Kubo A, Jwa NS, Tamogami S, Satoh K, Kikuchi S, Higashi T, Kimura S, Saji H, Tanaka Y, Iwahashi H, Masuo Y, Rakwal R (2008) Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. J Proteome Res 7:2980–2998

    Article  PubMed  CAS  Google Scholar 

  • Ehlting J, Provart NJ, Werck-Reichhart D (2006) Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis. Biochem Soc Trans 34:1192–1198

    Article  PubMed  CAS  Google Scholar 

  • Ehlting J, Sauveplane V, Olry A, Ginglinger JF, Provart NJ, Werck-Reichhart D (2008) An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. BMC Plant Biol 8:47

    Article  PubMed  CAS  Google Scholar 

  • Gachon CM, Langlois-Meurinne M, Henry Y, Saindrenan P (2005) Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. Plant Mol Biol 58:229–245

    Article  PubMed  CAS  Google Scholar 

  • Gigolashvili T, Berger B, Mock HP, Müller C, Weisshaar B, Flügge UI (2007a) The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana. Plant J 50:886–901

    Article  PubMed  CAS  Google Scholar 

  • Gigolashvili T, Yatusevich R, Berger B, Müller C, Flügge UI (2007b) The R2R3-MYB transcription factor HAG1/MYB28 is a regulator of methionine-derived glucosinolate biosynthesis in Arabidopsis thaliana. Plant J 51:247–261

    Article  PubMed  CAS  Google Scholar 

  • Gigolashvili T, Engqvist M, Yatusevich R, Müller C, Flügge UI (2008) HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. New Phytol 177:627–642

    Article  PubMed  CAS  Google Scholar 

  • Gigolashvili T, Berger B, Flügge UI (2009a) Specific and coordinated control of indolic and aliphatic glucosinolate biosynthesis by R2R3-MYB transcription factors in Arabidopsis thaliana. Phytochem Rev 8:3–13

    Article  CAS  Google Scholar 

  • Gigolashvili T, Yatusevich R, Rollwitz I, Humphry M, Gershenzon J, Flügge UI (2009b) The plastidic bile acid transporter 5 is required for the biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana. Plant Cell 21:1813–1829

    Article  PubMed  CAS  Google Scholar 

  • Grubb CD, Zipp BJ, Ludwig-Müller J, Masuno MN, Molinski TF, Abel S (2004) Arabidopsis glucosyltransferase UGT74B1 functions in glucosinolate biosynthesis and auxin homeostasis. Plant J 40:893–908

    Article  PubMed  CAS  Google Scholar 

  • Halkier BA, Gershenzon J (2006) Biology and biochemistry of glucosinolates. Annu Rev Plant Biol 57:303–333

    Article  PubMed  CAS  Google Scholar 

  • Hansen CH, Du L, Naur P, Olsen CE, Axelsen KB, Hick AJ, Pickett JA, Halkier BA (2001) CYP83b1 is the oxime-metabolizing enzyme in the glucosinolate pathway in Arabidopsis. J Biol Chem 276:24790–24796

    Article  PubMed  CAS  Google Scholar 

  • Hansen BG, Kliebenstein DJ, Halkier BA (2007) Identification of a flavin-monooxygenase as the S-oxygenating enzyme in aliphatic glucosinolate biosynthesis in Arabidopsis. Plant J 50:902–910

    Article  PubMed  CAS  Google Scholar 

  • Hansen BG, Kerwin RE, Ober JA, Lambrix VM, Mitchell-Olds T, Gershenzon J, Halkier BA, Kliebenstein DJ (2008) A novel 2-oxoacid-dependent dioxygenase involved in the formation of the goiterogenic 2-hydroxybut-3-enyl glucosinolate and generalist insect resistance in Arabidopsis. Plant Physiol 148:2096–2108

    Article  PubMed  CAS  Google Scholar 

  • He Y, Mawhinney TP, Preuss ML, Schroeder AC, Chen B, Abraham L, Jez JM, Chen S (2009) A redox-active isopropylmalate dehydrogenase functions in the biosynthesis of glucosinolates and leucine in Arabidopsis. Plant J 60:679–690

    Article  PubMed  CAS  Google Scholar 

  • Hemm MR, Ruegger MO, Chapple C (2003) The Arabidopsis ref2 mutant is defective in the gene encoding CYP83A1 and shows both phenylpropanoid and glucosinolate phenotypes. Plant Cell 15:179–194

    Article  PubMed  CAS  Google Scholar 

  • Hirai MY (2009) A robust omics-based approach for the identification of glucosinolate biosynthetic genes. Phytochem Rev 8:15–23

    Article  CAS  Google Scholar 

  • Hirai M, Klein M, Fujikawa Y, Yano M, Goodenowe D, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280:25590–25595

    Article  PubMed  CAS  Google Scholar 

  • Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa OI, Shibata D, Saito K (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA 104:6478–6483

    Article  PubMed  CAS  Google Scholar 

  • Hull AK, Vij R, Celenza JL (2000) Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc Natl Acad Sci USA 97:2379–2384

    Article  PubMed  CAS  Google Scholar 

  • Kliebenstein DJ, Lambrix VM, Reichelt M, Gershenzon J, Mitchell-Olds T (2001) Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis. Plant Cell 13:681–693

    Article  PubMed  CAS  Google Scholar 

  • Knill T, Schuster J, Reichelt M, Gershenzon J, Binder S (2008) Arabidopsis branched-chain aminotransferase 3 functions in both amino acid and glucosinolate biosynthesis. Plant Physiol 146:1028–1039

    Article  PubMed  CAS  Google Scholar 

  • Knill T, Reichelt M, Paetz C, Gershenzon J, Binder S (2009) Arabidopsis thaliana encodes a bacterial-type heterodimeric isopropylmalate isomerase involved in both Leu biosynthesis and the Met chain elongation pathway of glucosinolate formation. Plant Mol Biol 71:227–239

    Article  PubMed  CAS  Google Scholar 

  • Kroymann J, Textor S, Tokuhisa JG, Falk KL, Bartram S, Gershenzon J, Mitchell-Olds T (2001) A gene controlling variation in Arabidopsis glucosinolate composition is part of the methionine chain elongation pathway. Plant Physiol 127:1077–1088

    Article  PubMed  CAS  Google Scholar 

  • Kroymann J, Donnerhacke S, Schnabelrauch D, Mitchell-Olds T (2003) Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc Natl Acad Sci USA 100:14587–14592

    Article  PubMed  CAS  Google Scholar 

  • Li J, Hansen BG, Ober JA, Kliebenstein DJ, Halkier BA (2008) Subclade of flavin-monooxygenases involved in aliphatic glucosinolate biosynthesis. Plant Physiol 148:1721–1733

    Article  PubMed  CAS  Google Scholar 

  • Malitsky S, Blum E, Less H, Venger I, Elbaz M, Morin S, Eshed Y, Aharoni A (2008) The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators. Plant Physiol 148:2021–2049

    Article  PubMed  CAS  Google Scholar 

  • Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR (2006) Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res 34:W504–W509

    Article  PubMed  CAS  Google Scholar 

  • Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K (2009) AtMetExpress development: a phytochemical atlas of Arabidopsis thaliana development. Plant Physiol 152:566–578

    Article  PubMed  CAS  Google Scholar 

  • Mewis I, Tokuhisa JG, Schultz JC, Appel HM, Ulrichs C, Gershenzon J (2006) Gene expression and glucosinolate accumulation in Arabidopsis thaliana in response to generalist and specialist herbivores of different feeding guilds and the role of defense signaling pathways. Phytochemistry 67:2450–2462

    Article  PubMed  CAS  Google Scholar 

  • Mikkelsen MD, Petersen BL, Glawischnig E, Jensen AB, Andreasson E, Halkier BA (2003) Modulation of CYP79 genes and glucosinolate profiles in Arabidopsis by defense signaling pathways. Plant Physiol 131:298–308

    Article  PubMed  CAS  Google Scholar 

  • Mikkelsen MD, Naur P, Halkier BA (2004) Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis. Plant J 37:770–777

    Article  PubMed  CAS  Google Scholar 

  • Naur P, Petersen BL, Mikkelsen MD, Bak S, Rasmussen H, Olsen CE, Halkier BA (2003) CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis. Plant Physiol 133:63–72

    Article  PubMed  CAS  Google Scholar 

  • Obayashi T, Kinoshita K (2010) Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J Plant Res 123:311–319

    Article  PubMed  CAS  Google Scholar 

  • Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35:D863–D869

    Article  PubMed  CAS  Google Scholar 

  • Pfalz M, Vogel H, Kroymann J (2009) The gene controlling the indole glucosinolate modifier1 quantitative trait locus alters indole glucosinolate structures and aphid resistance in Arabidopsis. Plant Cell 21:985–999

    Article  PubMed  CAS  Google Scholar 

  • Piotrowski M, Schemenewitz A, Lopukhina A, Muller A, Janowitz T, Weiler EW, Oecking C (2004) Desulfoglucosinolate sulfotransferases from Arabidopsis thaliana catalyze the final step in the biosynthesis of the glucosinolate core structure. J Biol Chem 279:50717–50725

    Article  PubMed  CAS  Google Scholar 

  • Reintanz B, Lehnen M, Reichelt M, Gershenzon J, Kowalczyk M, Sandberg G, Godde M, Uhl R, Palme K (2001) Bus, a bushy Arabidopsis CYP79F1 knockout mutant with abolished synthesis of short-chain aliphatic glucosinolates. Plant Cell 13:351–367

    Article  PubMed  CAS  Google Scholar 

  • Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics—‘majority report by precogs’. Trends Plant Sci 13:36–43

    Article  PubMed  CAS  Google Scholar 

  • Sawada Y, Akiyama K, Sakata A, Kuwahara A, Otsuki H, Sakurai T, Saito K, Hirai MY (2009a) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol 50:37–47

    Article  PubMed  CAS  Google Scholar 

  • Sawada Y, Kuwahara A, Nagano M, Narisawa T, Sakata A, Saito K, Hirai MY (2009b) Omics-based approaches to methionine side chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase. Plant Cell Physiol 50:1181–1190

    Article  PubMed  CAS  Google Scholar 

  • Sawada Y, Toyooka K, Kuwahara A, Sakata A, Nagano M, Saito K, Hirai MY (2009c) Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis. Plant Cell Physiol 50:1579–1586

    Article  PubMed  CAS  Google Scholar 

  • Schneider A, Kirch T, Gigolashvili T, Mock HP, Sonnewald U, Simon R, Flügge UI, Werr W (2005) A transposon-based activation-tagging population in Arabidopsis thaliana (TAMARA) and its application in the identification of dominant developmental and metabolic mutations. FEBS Lett 579:4622–4628

    Article  PubMed  CAS  Google Scholar 

  • Schuster J, Knill T, Reichelt M, Gershenzon J, Binder S (2006) Branched-chain aminotransferase4 is part of the chain elongation pathway in the biosynthesis of methionine-derived glucosinolates in Arabidopsis. Plant Cell 18:2664–2679

    Article  PubMed  CAS  Google Scholar 

  • Shroff R, Vergara F, Muck A, Svatos A, Gershenzon J (2008) Nonuniform distribution of glucosinolates in Arabidopsis thaliana leaves has important consequences for plant defense. Proc Natl Acad Sci USA 105:6196–6201

    Article  PubMed  CAS  Google Scholar 

  • Smolen G, Bender J (2002) Arabidopsis cytochrome P450 cyp83B1 mutations activate the tryptophan biosynthetic pathway. Genetics 160:323–332

    PubMed  CAS  Google Scholar 

  • Sønderby IE, Hansen BG, Bjarnholt N, Ticconi C, Halkier BA, Kliebenstein DJ (2007) A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates. PLoS One 2:e1322

    Article  PubMed  CAS  Google Scholar 

  • Sønderby IE, Burow M, Rowe HC, Kliebenstein DJ, Halkier BA (2010) A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis. Plant Physiol 153:348–363

    Google Scholar 

  • Textor S, Bartram S, Kroymann J, Falk KL, Hick A, Pickett JA, Gershenzon J (2004) Biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana: recombinant expression and characterization of methylthioalkylmalate synthase, the condensing enzyme of the chain-elongation cycle. Planta 218:1026–1035

    Article  PubMed  CAS  Google Scholar 

  • Textor S, de Kraker JW, Hause B, Gershenzon J, Tokuhisa JG (2007) MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis. Plant Physiol 144:60–71

    Article  PubMed  CAS  Google Scholar 

  • Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, Noji M, Yamazaki M, Saito K (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J 42:218–235

    Article  PubMed  CAS  Google Scholar 

  • Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32:1633–1651

    Article  PubMed  CAS  Google Scholar 

  • Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, Langebartels C, Gruissem W, Inze D, Van Breusegem F (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol 139:806–821

    Article  PubMed  CAS  Google Scholar 

  • Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP, Somerville C, Loraine A (2006) Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol 142:762–774

    Article  PubMed  CAS  Google Scholar 

  • Wentzell AM, Kliebenstein DJ (2008) Genotype, age, tissue, and environment regulate the structural outcome of glucosinolate activation. Plant Physiol 147:415–428

    Article  PubMed  CAS  Google Scholar 

  • Yonekura-Sakakibara K, Tohge T, Niida R, Saito K (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem 282:14932–14941

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work was supported in part by the Core Research for Evolutional Science and Technology (CREST) of the Japan Science and Technology Agency (Project name: ‘Elucidation of Amino Acid Metabolism in Plants Based on Integrated Omics Analyses’).

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Affiliations

  1. RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Doris Albinsky, Yuji Sawada, Ayuko Kuwahara, Mutsumi Nagano, Akiko Hirai, Kazuki Saito & Masami Yokota Hirai

  2. JST, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama, 332-0012, Japan

    Doris Albinsky, Yuji Sawada, Ayuko Kuwahara, Mutsumi Nagano & Masami Yokota Hirai

  3. Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan

    Kazuki Saito

  4. Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan

    Masami Yokota Hirai

Authors
  1. Doris Albinsky
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  2. Yuji Sawada
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  3. Ayuko Kuwahara
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  4. Mutsumi Nagano
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  5. Akiko Hirai
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  6. Kazuki Saito
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  7. Masami Yokota Hirai
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Correspondence to Masami Yokota Hirai.

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D. Albinsky, Y. Sawada contributed equally to this work.

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Albinsky, D., Sawada, Y., Kuwahara, A. et al. Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the side-chain elongation steps of aliphatic glucosinolate biosynthesis. Amino Acids 39, 1067–1075 (2010). https://doi.org/10.1007/s00726-010-0681-5

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  • DOI: https://doi.org/10.1007/s00726-010-0681-5

Keywords

  • Glucosinolate biosynthesis
  • Widely targeted metabolomics
  • Batch-learning self-organising map (BL-SOM)
  • Side-chain elongation
  • Leucine biosynthesis