Abstract
The focus of this chapter is on gene families encoding enzymes of phenylpropanoid pathway in common bean. The introductory section contains a short overview of the phenylpropanoid pathway. Section 11.2 introduces major gene families encoding enzymes of this pathway in common bean, soybean, and Arabidopsis in the current annotations of their complete genome sequences (Phaseolus vulgaris v1.0, Glycine max Wm82.a2.v1, and Arabidopsis thaliana TAIR10) deposited in Phytozome 10.2. For each of the 21 enzyme classes, their functional annotations were based on the commonly used Pfam and KOG databases, while the number of genes in each family was based on Phytozome and KEGG databases. Section 11.3 describes cytochrome P450s involved in the phenylpropanoid pathway with particular emphasis on ten families included in the general (central) phenylpropanoid pathway, C4H (family CYP73A), in the lignin/lignan branch, C3H (family CYP98A) and F5H (family CYP84A), in the flavonoid/anthocyanin/proanthocyanidin branch, F3′H (family CYP75B), F3′5′H (family CYP75A), and FNS (family CYP93B), and in the isoflavonoid branch IFS (family CYP93C), I2′H (family CYP81E), F6H (family CYP71D), and D6aH (family CYP93A). The availability of the complete genome sequences enabled a thorough inventory of putative P450 genes encoding enzymes of this metabolic pathway. The P450 gene sequences from common bean were compared to homologs from Arabidopsis and soybean and confirmed with the information published for both soybean and common bean genomes. Cinnamate 4-hydroxylase (C4H) is the first P450 enzyme in the phenylpropanoid pathway and is described in detail in Sect. 11.4. It belongs to the relatively small CYP73A gene family. Genome locations and gene structures including cis-regulatory regions in 5′UTRs (5′ regulatory sequences) are detailed for this family in common bean. In addition, the expression patterns of these genes in different tissues (Phytozome 10.2) and syntenic relationships (Plant Genome Duplication Database) between common bean and soybean were examined. Finally, genes encoding the C4H enzyme in landrace G19833 (Andean gene pool, Phytozome 10.2) and in cultivar OAC Rex (Mesoamerican gene pool) were compared and searched for polymorphisms. These sequence differences can be used to develop C4H gene-based marker(s) to explore the roles of these genes in various processes such as lignin or anthocyanin biosynthesis.
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References
Adlercreutz H (2007) Lignans and human health. Crit Rev Clin Lab Sci 44:483–525
Agati G, Azzarello E, Pollastri S, Tattini M (2012) Flavonoids as antioxidants in plants: location and functional significance. Plant Sci 196:67–76
Agati G, Brunetti C, Di Ferdinando M, Ferrini F, Pollastri S, Tattini M (2013) Functional roles of flavonoids in photoprotection: new evidence, lessons from the past. Plant Physiol Biochem 72:35–45
Aguade M (2001) Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the Fah1and F3Hgenes, in Arabidopsis thaliana. Mol Biol Evol 18:1–9
Akada S, Dube SK (1995) Organization of soybean chalcone synthase gene clusters and characterization of a new member of the family. Plant Mol Biol 29:189–199
Akashi T, Aoki T, Ayabe S (2005) Molecular and biochemical characterization of 2-hydroxyisoflavanone dehydratase. Involvement of carboxylesterase-like proteins in leguminous isoflavone biosynthesis. Plant Physiol 137:882–891
Alber A, Ehlting J (2012) Cytochrome P450s in lignin biosynthesis. Adv Bot Res 61:113–143
Anterola AM, Lewis NG (2002) Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61:221–294
Artigot M-P, Dayde J, Berger M (2013) Expression of flavonoid 6-hydroxylase candidate genes in normal and mutant soybean genotypes for glycitein content. Mol Biol Rep 40:4361–4369
Austin MB, Noel JP (2003) The chalcone synthase superfamily of type III polyketide synthases. Nat Prod Rep 20:79–110
Ayabe S, Akashi T (2006) Cytochrome P450s in flavonoid metabolism. Phytochem Rev 5:271–282
Bak S, Beisson F, Hamberger B, Hofer R, Paquette S, Werck-Reichhart D (2011) Cytochrome P450. Arabidopsis Book 9:e0144. doi:10.1199/tab.0144
Barakat A, Bagniewska-Zadworna A, Frost CJ, Carlson JE (2010) Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides × P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence. BMC Plant Biol 10:100. doi:10.1186/1471-2229-10-100
Barker MS, Baute GJ, Liu S-L (2012) Duplications and turnover in plant genomes. In: Wendel JF, Greilhuber J, Dolezal J, Leitch IJ (eds) Plant genome diversity, vol 1. Springer-Verlag, Wien, pp 155–169
Bassard J-E, Richert L, Geerinck J, Renault H, Duval F, Ullmann P, Schmitt M, Meyer E, Mutterer J, Boerjan W, De Jaeger G, Mely Y, Goossens A, Werck-Reichhart D (2012) Protein-protein and protein-membrane associations in the lignin pathway. Plant Cell 24:4465–4482
Baxter HL, Stewart N Jr (2013) Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress. Biofuels 4:635–650
Bell-Lelong DA, Cusumano JC, Meyer K, Chapple C (1997) Cinnamate-4-hydroxylase expression in Arabidopsis. Regulation in response to development and the environment. Plant Physiol 113:729–738
Blee K, Choi JW, O’Connell AP, Jupe SC, Schuch W, Lewis NG, Bolwell GP (2001) Antisense and sense expression of cDNA coding for CYP73A15, a class II cinnamate 4-hydroxylase, leads to a delayed and reduced production of lignin in tobacco. Phytochemistry 57:1159–1166
Boerjan W, Ralp J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546. doi:10.1146/annurev.arplant.54.031902.134938
Brenner EA, Zein I, Chen Y, Andersen JR, Wenzel G, Ouzunova M, Eder J, Darnhofer B, Frei U, Barriere Y, Lubberstedt T (2010) Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.). BMC Plant Biol 10:27. doi:10.1186/1471-2229-10-27
Brunetti C, Di Ferdinando M, Fini A, Pollastri S, Tattini M (2013) Flavonoids as antioxidants and developmental regulators: relative significance in plants and humans. Int J Mol Sci 14:3540–3555. doi:10.3390/ijms14023540
Cassidy A, Hanley B, Lamuela-Raventos RM (2000) Isoflavones, lignans and stilbenes—origins, metabolism and potential importance to human health. J Sci Food Agric 80:1044–1062
Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 7:R13
Chen J, Wang L, Thompson LU (2006) Flaxseed and its components reduce metastasis after surgical excision of solid human breast tumor in nude mice. Cancer Lett 234:168–175
Cheynier V, Comte G, Davies KM, Lattanzio V, Martens S (2013) Plant phenolics: recent advances on their biosynthesis, genetics, and ecophysiology. Plant Physiol Biochem 72:1–20
Chu S, Wang J, Cheng H, Yang Q, Yu D (2014) Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean. BMC Genet 15:76
Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG (2003) An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof. Phytochemistry 64:1097–1112
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190
Dhaubhadel S (2011) Regulation of isoflavonoid biosynthesis in soybean seeds. In: Ng T-B (ed) Soybean—biochemistry, chemistry and physiology. InTech, http://www.intechopen.com
Ehlting J, Hamberger B, Milliom-Rousseau R, Werck-Reichhart D (2006) Cytochrome P450 in phenolic metabolism. Phytochem Rev 5:239–270
Ehlting J, Sauveplane V, Olry A, Ginglinger J-F, 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. doi:10.1186/1471-2229-8-47
Falcone Ferreyra ML, Rius SP, Casati P (2012) Flavonoids: biosynthesis, biological functions, and biotechnological applications. Front Plant Sci 3:222. doi:10.3389/fpls.2012.00222
Ferrer JL, Austin MB, Stewart C Jr, Noel JP (2008) Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol Biochem 46:356–370. doi:10.1016/j.plaphy.2007.12.009
Fraser CM, Chapple C (2011) The phenylpropanoid pathway in Arabidopsis. Arabidopsis Book 9:e0152. doi:10.1199/tab.0152
Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental or by transposition. Annu Rev Plant Biol 60:433–453
Galeano CH, Fernandez AC, Gomez M, Blair MW (2009) Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genom 10:629. doi:10.1186/1471-2164-10-629
Garnier J, Gibrat JF, Robson B (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266:540–553
Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53:814–827
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186
Gou J-Y, Felippes FF, Liu C-J, Weigel D, Wang J-W (2011) Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 23:1512–1522
Goujon T, Sibout R, Eudes A, MacKay J, Jouanin L (2003) Genes involved in the biosynthesis of lignin precursors in Arabidopsis thaliana. Plant Physiol Biochem 41:677–687
Graham SE, Peterson JA (1999) How similar are P450s and what can their differences teach us? Arch Biochem Biophys 369:24–29
Graham T, Graham M, Yu O (2008) Genomics of secondary metabolism in soybean. In: Stacey G (ed) Genetics and genomics of soybean. Springer Science+Business Media, LLC, Berlin, pp 211–241
Grotewold E (2005) Plant metabolic diversity: a regulatory perspective. Trends Plant Sci 10:57–62
Guttikonda SK, Trupti J, Bisht NC, Chen H, An Y-QC, Pandey S, Xu D, Yu O (2010) Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. BMC Plant Biol 12:243
Hahlbrock K, Scheel D (1989) Physiology and molecular biology of phenylpropanoid metabolism. Annu Rev Plant Physiol Plant Mol Biol 40:347–369
Hamberger B, Bak S (2013) Plant P450s as versatile drivers for evolution of species-specific chemical diversity. Philos Trans R Soc B 368:20120426
Hamberger B, Ellis M, Friedmann M, de Azevedo Souza C, Barbazuk B, Douglas CJ (2007) Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene families. Can J Bot 85:1182–1201
Hanada K, Sawada Y, Kuromori T, Klausnitzer R, Saito K, Toyoda T, Shinozaki K, Li W-H, Hirai MY (2011) Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol Biol Evol 28:377–382
Hao Z, Mohnen D (2014) A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes. Crit Rev Biochem Mol Biol 49:212–241
Harakava R (2005) Genes encoding enzymes of the lignin biosynthesis pathway in Eucalyptus. Genet Mol Biol 28:601–607
Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B (2005) Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant Mol Biol 57:155–171
Hawkins T, Chitale M, Luban S, Kihara D (2009) PFP: automated prediction of Gene Ontology functional annotations with confidence scores using protein sequence data. Proteins 74:566–582
Hrazdina G, Wagner GJ (1985) Metabolic pathways as enzyme complexes: evidence for the synthesis of phenylpropanoids and flavonoids on membrane associated enzyme complexes. Arch Biochem Biophys 237:88–100
Humphreys JM, Hemm MR, Chapple C (1999) New routes for lignin biosynthesis defined by biochemical characterization of recombinant ferulate 5-hydroxylase, a multifunctional cytochrome P450-dependent monooxygenase. Proc Natl Acad Sci U S A 96:10045–10050
Humphreys JM, Chapple C (2002) Rewriting the lignin roadmap. Curr Opin Plant Biol 5:224–229
Jung W, Yu O, Lau SM, O’Keefe DP, Odell J, Fader G, McGonigle B (2000) Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes. Nat Biotechnol 18:208–212
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:45–858. doi:10.1038/nprot.2015.053
Koes R, Verweij W, Quattrocchio F (2005) Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci 10:236–242
Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580. doi:10.1006/jmbi.2000.4315
Kumar MS, Chakravarthy SS, Babu PR, Rao KV, Reddy VD (2015) Classification of cytochrome P450s in common bean (Phaseolus vulgaris L.). Plant Syst Evol 301:211–216
Labeeuw L, Martone LT, Boucher Y, Case RJ (2015) Ancient origin of the biosynthesis of lignin precursors. Biol Direct 10:23. doi:10.1186/s13062-015-0052-y
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210
Latunde-Dada AO, Cabello-Hurtado F, Czittrich N, Didierjean L, Schopfer C, Hertkorni N, Werck-Reichhart D, Ebel J (2001) Flavonoid 6-hydroxylase from soybean (Glycine max L.), a novel plant P-450 monooxygenase. J Biol Chem 276:1688–1695
Lee TH, Tang H, Wang X, Paterson AH (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res. doi:10.1093/nar/gks1104
Lescot M, Déhais P, Moreau Y, De Moor B, Rouzé P, Rombauts S (2002) PlantCARE: a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325–327
Li S (2014) Transcriptional control of flavonoid biosynthesis—fine-tuning of the MYB-bHLH-WD40 (MBW) complex. Plant Sig Behav 9:e27522
Lozovaya VV, Lygin AV, Zernova OV, Ulanov AV, Li S, Hartman GL, Widholm JM (2007) Modification of phenolic metabolism in soybean hairy roots through down regulation of chalcone synthase or isoflavone synthase. Planta 225:665–679
Lu S, Zhou Y, Li L, Chiang VL (2006) Distinct roles of cinnamate 4-hydroxylase genes in Populus. Plant Cell Physiol 47:905–914
Lucheta AR, Silva-Pinhati ACO, Basílio-Palmieri AC, Berger IJ, Freitas-Astúa J, Cristofani M (2007) An in silico analysis of the key genes involved in flavonoid biosynthesis in Citrus sinensis. Genet Mol Biol 30:819–831
Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:151–1155
Matsumura H, Watanabe S, Harada K, Senda M, Akada S, Kawasaki S, Dubouzet EG, Minaka N, Takahashi R (2005) Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean. Theor Appl Genet 110:1203–1209
Matsuno M, Compagnon V, Schoch GA, Schmitt M, Debayle D, Bassard J-E, Pollet B, Hehn A, Heintz D, Ullmann P, Lapierre C, Bernier F, Ehlting J, Werck-Reichhart D (2009) Evolution of a novel phenolic pathway for pollen development. Science 324:1688–1692
McClean PE, Mamidi S, McConnell M, Chikara S, Lee R (2010) Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genom 11:184. doi:10.1186/1471-2164-11-184
Miedes E, Vanholme R, Boerjan W, Molina A (2014) The role of the secondary cell wall in plant resistance to pathogens. Front Plant Sci 5:358. doi:10.3389/fpls.2014.00358
Mizutani M (2012) Impacts of diversification of cytochrome P450 on plant metabolism. Biol Pharm Bull 35:824–832
Mizutani M, Ohta D (2010) Diversification of P450 genes during land plant evolution. Annu Rev Plant Biol 61:291–315
Mizutani M, Ohta D, Sato R (1997) Isolation of a cDNA and a genomic clone encoding cinnamate 4-hydroxylase from Arabidopsis and its expression manner in plants. Plant Physiol 113:755–763
Mizutani M, Sato F (2011) Unusual P450 reactions in plant secondary metabolism. Arch Biochem Biophys 507:94–203
Mizutani M, Ward E, DiMaio J, Ohta D Ryals J, Sato R (1993) Molecular cloning and sequencing of a cDNA encoding mung bean cytochrome P450 (P450C4H) possessing cinnamate 4-hydroxylase activity. Biochem Biophys Res Commun 190:875–880
Moura JC, Bonine CA, de Oliveira Fernandes Viana J, Dornelas MC, Mazzafera P (2010) Abiotic and biotic stresses and changes in the lignin content and composition in plants. J Integr Plant Biol 52:360–376. doi:10.1111/j.1744-7909.2010.00892.x
Nagano S (2014) Structural and functional diversity of cytochrome P450. In: Yamazaki H (ed) Fifty years of cytochrome P450 research. Springer, Japan, pp 95–106. doi:10.1007/978-4-431-54992-5_5
Naoumkina MA, Zhao Q, Gallego-Giraldo L, Dai X, Zhao PX, Dixon RA (2010) Genome-wide analysis of phenylpropanoid defence pathways. Mol Plant Pathol 11:829–846
Nedelkina S, Jupe SC, Blee KA, Schalk M, Werck-Reichhart D, Bolwell GP (1999) Novel characteristics and regulation of a divergent cinnamate 4-hydroxylase (CYP73A15) from French bean: engineering expression in yeast. Plant Mol Biol 39:1079–1090
Nelson DR (2006) Cytochrome P450 nomenclature, 2004. Method Mol Biol 320:1–10
Nelson DR (2009) The cytochrome P450 homepage. Hum Genomics 4:59–65
Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, Waterman MR, Gotoh O, Coon MJ, Estabrook RW, Gunsalus IC, Nebert DW (1996) P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6:1–42
Nelson DR, Ming R, Alam M, Schuler MA (2008) Comparison of cytochrome P450 genes from six plant genomes. Trop Plant Biol 1:216–235
Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S (2004) Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiol 135:756–772
Nelson DR, Werck-Reichhart D (2011) A P450-centric view of plant evolution. Plant J 66:194–211
Noel JP, Austin MB, Bomati EK (2005) Structure-function relationships in plant phenylpropanoid biosynthesis. Curr Opin Plant Biol 8:249–253
Nutzmann H-W, Osbourn A (2014) Gene clustering in plant specialized metabolism. Curr Opin Biotechnol 26:91–99
Nutzmann H-W, Osbourn A (2015) Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytol 205:503–510. doi:10.1111/nph.13189
O’Rourke JA, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, McClean PE, Li J, Dai X, Zhao PX, Hernandez G, Vance CP (2014) An RNA-Seq based gene expression atlas of the common bean. BMC Genom 15:866
Osakabe K, Tsao CC, Li L, Popko JL, Umezawa T, Carraway DT, Smeltzer RH, Joshi CP, Chiang VL (1999) Coniferyl aldehyde 5-hydroxylation and methylation direct syringyl lignin biosynthesis in angiosperms. Proc Natl Acad Sci U S A 96:8955–8960
Paquette SM, Jensen K, Bak S (2009) A web-based resource for the Arabidopsis P450, cytochromes b5, NADPH-cytochrome P450 reductases, and family 1 glycosyltransferases (http://www.P450.kvl.dk). Phytochemistry 70:1940–1947
Parvathi K, Chen F, Guo D, Blount JW, Dixon RA (2001) Substrate preferences of O-methyltransferases in alfalfa suggest new pathways for 3-O-methylation of monolignols. Plant J 25:193–202
Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC (2006) Many genes and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet 22:597–602
Petrussa E, Braidot E, Zancani M, Peresson C, Bertolini A, Patui S, Vianello A (2013) Plant flavonoids-Biosynthesis, transport and involvement in stress responses. Int J Mol Sci 14:14950–14973. doi:10.3390/ijms140714950
Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W (2003) Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol 133:1051–1071
Ralston L, Subramanian S, Matsuno M, Yu O (2005) Partial reconstruction of flavonoid and isoflavonoid biosynthesis in yeast using soybean type I and type II chalcone isomerases. Plant Physiol 137:1375–1388
Ralston L, Yu O (2006) Metabolons involving plant cytochrome P450s. Phytochem Rev 5:459–472
Ramsay NA, Glover BJ (2005) MYB-bHLH-WD40 protein complex and the evolution of cellular diversity. Trends Plant Sci 10:63–70
Reinprecht Y, Yadegari Z, Perry GE, Siddiqua M, Wright LC, McClean PE, Pauls KP (2013) In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr. Front Plant Sci 4:317. doi:10.3389/fpls.2013.00317
Rupasinghe S, Baudry J, Mary A, Schuler MA (2003) Common active site architecture and binding strategy of four phenylpropanoid P450s from Arabidopsis thaliana as revealed by molecular modeling. Protein Eng 16:721–731. doi:10.1093/protein/gzg094
Ryder TB, Hedrick SA, Bell JN, Liang XW, Clouse SD, Lamb CJ (1987) Organization and differential activation of a gene family encoding the plant defense enzyme chalcone synthase in Phaseolus vulgaris. Mol Gen Genet 210:219–233
Saito K, Yonekura-Sakakibara K, Nakabayashi R, Higashi Y, Yamazaki M, Tohge T, Fernie AR (2013) The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Plant Physiol Biochem 72:21–34
Savolainen O, Langley CH, Lazzaro BP, Freville H (2000) Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. Mol Biol Evol 17:645–655
Schilmiller AL, Stout J, Weng J-K, Humphreys J, Ruegger MO, Chapple C (2009) Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J 60:771–782
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713
Schoch G, Goepfert S, Morant M, Hehn A, Meyer D, Ullmann P, Werck-Reichhart D (2001) CYP98A3 from Arabidopsis thaliana is a 3′-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway. J Biol Chem 276:36566–36574
Schopfer CR, Ebel J (1998) Identification of elicitor-induced cytochrome P450s of soybean (Glycine max L.) using differential display of mRNA. Mol Gen Genet 258:315–322
Schuler MA, Werck-Reichhart D (2003) Functional genomics of P450s. Annu Rev Plant Biol 54:629–667
Schuler MA, Duan H, Bilgin M, Ali S (2006) Arabidopsis cytochrome P450s through the looking glass: a window on plant biochemistry. Phytochem Rev 5:205–237
Senda M, Jumonji A, Yumoto S, Ishikawa R, Harada T, Niizeki M, Akada S (2002) Analysis of the duplicated CHS1 gene related to the suppression of the seed coat pigmentation in yellow soybeans. Theor Appl Genet 104:1086–1091
Severin AJ, Woody JL, Bolon Y-T, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC (2010) RNA-Seq atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:160
Sewalt VJH, Ni W, Blount JW, Jung HG, Masoud SA, Howles PA, Lamb C, Dixon RA (1997) Reduced lignin content and altered lignin composition in transgenic tobacco down-regulated in expression of l-phenylalanine ammonia-lyase or cinnamate 4-hydroxylase. Plant Physiol 115:41–50
Sezutsu H, Le Goff G, Feyereisen R (2013) Origins of P450 diversity. Philos Trans R Soc B 368:20120428
Shelton D, Stranne M, Mikkelsen L, Pakseresht N, Welham T, Hiraka H, Tabata S, Sato S, Paquette S, Wang TL, Martin C, Bailey P (2012) Transcription factors of lotus: regulation of isoflavonoid biosynthesis requires coordinated changes in transcription factor activity. Plant Physiol 159:531–547
Shi R, Sun Y-H, Li Q, Heber S, Seferoff R, Chiang VL (2010) Towards a system approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant Cell Physiol 51:144–163
Shimamura M, Akashi T, Sakurai N, Suzuki H, Saito K, Shibata D, Ayabe S, Aoki T (2007) 2-hydroxyisoflavanone dehydratase is a critical determinant of isoflavone productivity in hairy root cultures of Lotus japonicus. Plant Cell Physiol 48:1652–1657
Soderlund C, Bomhoff M, Nelson WM (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res 39:e68. doi:10.1093/nar/gkr123
Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7:S10. doi:10.1186/gb-2006-7-s1-s10
Steele CL, Gijzen M, Qutob D, Dixon RA (1999) Molecular characterization of the enzyme catalyzing the aryl migration reaction of isoflavonoid biosynthesis in soybean. Arch Biochem Biophys 367:146–150
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetic analysis version 6.0. Mol Biol Evol 30:2725–2829
Tanaka Y (2006) Flower colour and cytochromes P450. Phytochem Rev 5:283–291. doi:10.1007/s11101-006-9003-7
Tanaka Y, Brugliera F (2013) Flower colour and cytochromes P450. Philos Trans R Soc Lond B Biol Sci 368:20120432. doi:10.1098/rstb.2012.0432
Teutsch HG, Hasenfratz M, Lesot A, Stoltz C, Garnier J-M, Jeltsch J-M, Durst F, Werck-Reichhart D (1993) Isolation and sequence of a cDNA encoding the Jerusalem artichoke cinnamate 4-hydroxylase, a major plant cytochrome P450 involved in the general phenylpropanoid pathway. Proc Natl Acad Sci U S A 90:4102–4106
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Tohge T, Watanabe M, Hoefgen R, Fernie AR (2013) The evolution of phenylpropanoid pathway in the green lineage. Crit Rev Biochem Mol Biol 48:123–152
Tohge T, Yonekura-Sakakibara K, Niida R, Watanabe-Takahashi A, Saito K (2007) Phytochemical genomics in Arabidopsis thaliana: a case study for functional identification of flavonoid biosynthesis genes. Pure Appl Chem 79:811–823
Tsai C-J, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y (2006) Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus. New Phytol 172:47–62. doi:10.1111/j.1469-8137.2006.01798.x
Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W (2010) Lignin biosynthesis and structure. Plant Physiol 153:895–905
Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3:2–20
Wang X (2011) Structure, function, and engineering of enzymes in isoflavonoid biosynthesis. Funct Integr Genomics 11:13–22
Wang Y, Tan X, Paterson AH (2013) Different patterns of gene structure divergence following gene duplication in Arabidopsis. BMC Genom 14:652
Wang Y, Wang X, Paterson AH (2012) Genome and gene duplications and gene expression divergence: a view from plats. Ann N Y Acad Sci 1256:1–14
Weng J-K, Chapple C (2010) The origin and evolution of lignin biosynthesis. New Phytol 187:273–285
Werck-Reichhart D (1995) Cytochromes P450 in phenylpropanoid metabolism. Drug Metabol Drug Interact 12:221–243
Werck-Reichhart D, Feyereisen R (2000) Cytochrome P450: a success story. Genome Biol 1:reviews3003.1–reviews3003.9
Winkel-Shirley B (1999) Evidence for enzyme complexes in the phenylpropanoid and flavonoid pathways. Physiol Plant 107:142–149
Winkel-Shirley B (2001) Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 126:485–493
Wright SI, Lauga B, Charlesworth D (2003) Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Mol Ecol 12:1247–1263
Xiao CW (2008) Health effects of soy protein and isoflavones in humans. J Nutr 138:1244S–1249S
Xu Z, Zhang D, Hu J, Zhou X, Ye X, Reichel KL, Stewart NR, Syrenne RD, Yang X, Gao P, Shi W, Doeppke C, Sykes RW, Burris JN, Bozell JJ, Cheng Z-M, Hayes DG, Labbe N, Davis M, Stewart CN, Yuan JS (2009) Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. BMC Bioinform 10:S3
Xu W, Dubos C, Lepiniec L (2015) Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci 20:176–185
Xu W, Grain D, Bobet S, Le Gourrierec J, Thevenin J, Kelemen Z, Lepiniec L, Dubos C (2014) Complexity and robustness of the flavonoid transcriptional regulatory network revealed by comprehensive analyses of MYB-bHLH-WDR complexes and their targets in Arabidopsis seed. New Phytol 202:132–144. doi:10.1111/nph.12620
Yadegari Z (2013) Molecular mapping and characterization of phenylpropanoid pathway genes in common bean (Phaseolus vulgaris L.). Ph.D. thesis, University of Guelph, Guelph, Canada
Yi J, Derynck MR, Chen L, Dhaubhadel S (2010a) Differential expression of CHS7 and CHS8 genes in soybean. Planta 231:741–753
Yi J, Derynck MR, Li X, Telmer P, Marsolais F, Dhaubhadel S (2010b) A single repeat MYB transcription factor, GmMYB176, regulates CHS8 gene expression and affects isoflavonoid biosynthesis in soybean. Plant J 62:1019–1034
Yoon J, Choi H, An G (2015) Roles of lignin biosynthesis and regulatory genes in plant development. J Integr Plant Biol 57:902–912
Zhao Q, Dixon RA (2011) Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends Plant Sci 16:227–233
Zhong R, Ye Z-H (2009) Transcriptional regulation of lignin biosynthesis. Plant Signal Behav 4:1028–1034
Zubieta C, Parvathi K, Ferrer J-L, Dixon RA, Noel JP (2002) Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid3/5-O-methyltransferase. Plant Cell 14:1265–1277
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Reinprecht, Y., Perry, G.E., Peter Pauls, K. (2017). A Comparison of Phenylpropanoid Pathway Gene Families in Common Bean. Focus on P450 and C4H Genes. In: Pérez de la Vega, M., Santalla, M., Marsolais, F. (eds) The Common Bean Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-63526-2_11
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