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Molecular Characterization of Soybean Pterocarpan 2-Dimethylallyltransferase in Glyceollin Biosynthesis: Local Gene and Whole-Genome Duplications of Prenyltransferase

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Molecular Characterization of Soybean Pterocarpan 2-Dimethylallyltransferase in Glyceollin Biosynthesis: Local Gene and Whole-Genome Duplications of Prenyltransferase Molecular Characterization of Soybean Pterocarpan 2-Dimethylallyltransferase in Glyceollin Biosynthesis: Local Gene and Whole-Genome Duplications of Prenyltransferase Genes Led to the Structural Diversity of Soybean Regular Paper Prenylated Isoflavonoids Keisuke Yoneyama, Tomoyoshi Akashi and Toshio Aoki* Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan *Corresponding author: E-mail, [email protected]; Fax, +81-466-84-3353. (Received August 2, 2016; Accepted October 15, 2016) Soybean (Glycine max) accumulates several prenylated iso- HPT, homogentisate phytyltransferase; IDT, isoflavone flavonoid phytoalexins, collectively referred to as glyceollins. dimethylallyltransferase; IFS, 2-hydroxyisoflavanone synthase; Glyceollins (I, II, III, IV and V) possess modified pterocarpan LGD, local gene duplication; m/z, mass to-charge ratio; MS/ skeletons with C5 moieties from dimethylallyl diphosphate, MS, tandem mass spectrometry; NCBI, the National Center for and they are commonly produced from (6aS, 11aS)-3,9,6a- Biotechnology Information, NMR, nuclear magnetic resonance; trihydroxypterocarpan [(À)-glycinol]. The metabolic fate of P450, cytochrome P450 monooxygenase; P6aH, pterocarpan (À)-glycinol is determined by the enzymatic introduction of 6a-hydroxylase; PT, prenyltransferase; TLC, thin-layer chroma- a dimethylallyl group into C-4 or C-2, which is reportedly tography; TQMS, triple quadrupole mass spectrometry; catalyzed by regiospecific prenyltransferases (PTs). 4- TMHMM, transmembrane hidden Markov model; UPLC, Dimethylallyl (À)-glycinol and 2-dimethylallyl (À)-glycinol ultra-performance liquid chromatography; WGD, whole- are precursors of glyceollin I and other glyceollins, respect- genome duplication. ively. Although multiple genes encoding (À)-glycinol biosyn- All nucleotide sequences reported in this paper have been thetic enzymes have been identified, those involved in the submitted to the DDBJ/EMBL/GenBank database under acces- later steps of glyceollin formation mostly remain unidenti- sion numbers LC140926 (PT3), LC140927 (C4DT), LC140928 fied, except for (À)-glycinol 4-dimethylallyltransferase (IDT1), LC140929 (IDT2) and LC140930 (G2DT). (G4DT), which is involved in glyceollin I biosynthesis. In this study, we identified four genes that encode isoflavonoid PTs, including (À)-glycinol 2-dimethylallyltransferase Introduction (G2DT), using homology-based in silico screening and bio- chemical characterization in yeast expression systems. Flavonoids comprise a widespread class of plant metabolites, Transcript analyses illustrated that changes in G2DT gene and those with one or more dimethylallyl (C5) or geranyl (C10) expression were correlated with the induction of glyceollins groups present on their aromatic rings are known as prenylated II, III, IV and V in elicitor-treated soybean cells and leaves, flavonoids. The structures of prenylated flavonoids vary regard- suggesting its involvement in glyceollin biosynthesis. ing the numbers and lengths of prenyl groups and modifica- Moreover, the genomic signatures of these PT genes revealed tions such as cyclization and hydroxylation. Hence, prenylated that G4DT and G2DT are paralogs derived from whole- flavonoids are highly diverse, and they include approximately genome duplications of the soybean genome, whereas 1,000 compounds that are increasingly examined for their anti- other PT genes [isoflavone dimethylallyltransferase 1 (IDT1) oxidant, antitumor, antibacterial, antiviral and estrogenic activ- and IDT2] were derived via local gene duplication on soy- ities (Yazaki et al. 2009). Although some of the properties are bean chromosome 11. common to flavonoids with no prenyl groups, it is generally accepted that prenyl moieties increase lipophilicity and mem- Keywords: Gene duplication Isoflavonoid Phytoalexin brane permeability, and tend to potentiate the bioactivities of Prenyltransferase Soybean. flavonoids (Botta et al. 2005, Yazaki et al. 2009, Yang et al. 2015). Abbreviations: C4DT, coumestrol 4-dimethylallyltransferase; Prenylation of flavonoids is catalyzed by prenyltransferases CDS, coding sequence; DMAPP, dimethylallyl diphosphate; (PTs), which transfer prenyl moieties from allylic prenyl diphos- ESI, electrospray ionization; EST, expressed sequence tag; phate to flavonoid skeletons. The flavonoid-specific PT narin- G2DT, (À)-glycinol 2-dimethylallyltransferase; G4DT, (À)-glyci- genin 8-dimethylallyltransferase (SfN8DT) was initially nol 4-dimethylallyltransferase; HGGT, homogentisate geranyl- identified in the leguminous plant Sophora flavescens (Sasaki geranyltransferase; HID, 2-hydroxyisoflavanone dehydratase; et al. 2008), and several plant PTs that act on flavonoids and Plant Cell Physiol. 57(12): 2497–2509 (2016) doi:10.1093/pcp/pcw178, available online at www.pcp.oxfordjournals.org ! The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] K. Yoneyama et al. | Soybean isoflavonoid prenyltransferases Fig. 1 Biosynthetic pathways of prenylated isoflavonoids in soybean. Bold arrows show reactions catalyzed by the PTs that were characterized in this study. As the candidates of IDT1 and IDT2 products, 30-dimethylallyldaidzein, 30-dimethylallylgenistein and 8-dimethylallyldaidzein were identified in soybean (Cheng et al. 2011), but the genuine products of IDT1 and IDT2 were not determined. The other PT products have been reported. See text. Dashed arrows represent putative steps. C4DT, coumestrol 4-dimethylallyltransferase; G2DT, (À)-glycinol 2-dimethylallyl- transferase; G4DT, (À)-glycinol 4-dimethylallyltransferase; IDT1, isoflavone dimethylallyltransferase 1; IDT2, isoflavone dimethylallyltransferase 2; IFS, 2-hydroxyisoflavanone synthase; HID, 2-hydroxyisoflavanone dehydratase; P6aH, pterocarpan 6a-hydroxylase. other aromatic compounds have been molecularly and bio- et al. 2000). More than half of these isoflavonoids are preny- chemically characterized (Akashi et al. 2009, Sasaki et al. 2011, lated, and many prenylated isoflavonoids are considered to be Shen et al. 2012, Chen et al. 2013, Karamat et al. 2014, Li et al. inducible antimicrobial phytoalexins. Glyceollins, a series of 2014, Munakata et al. 2014, Wang et al. 2014, Li et al. 2015, prenylated pterocarpans, are well known to be the phytoalexins Munakata et al. 2016). A recent report on hop PTs demon- of soybean (Glycine max) (Tahara and Ibrahim 1995). During strated that a complex of two PTs, as a metabolon, catalyzes glyceollin biosynthesis, the dimethylallyl moiety is introduced three steps of sequential aromatic prenylation in b-bitter acid at either C-4 or C-2 of the pterocarpan precursor (À)-glycinol biosynthesis (Li et al. 2015). However, there is a wide gap be- [(6aS, 11aS)-3,9,6a-trihydroxypterocarpan; Fig. 1]. Although tween the number of identified PTs and that of known preny- most glycinol biosynthetic enzymes and their genes have lated flavonoids and aromatic compounds. The fact that these been characterized, little is known about the enzymes respon- characterized PTs have stringent substrate specificities indi- sible for the succeeding prenylation and cyclization reactions, cates the presence of additional unidentified PTs. which lead to the formation of the characteristic structure of Isoflavonoids comprise a subclass of flavonoids, in which glyceollins. A homology-based approach has led to the isolation phenyl rings (B-rings) are attached to C-3 instead of C-2 in of a cDNA encoding dimethylallyl diphosphate (DMAPP):(À)- the flavonoid skeleton. Isoflavonoids are further classified as glycinol 4-dimethylallyltransferase (G4DT), which yields 4- isoflavones, pterocarpans, coumestans or isoflavans, all of dimethylallylglycinol, the direct precursor of glyceollin I which are predominantly unique to leguminous plants (Aoki (Akashi et al. 2009), but not 2-dimethylallylglycinol, suggesting 2498 Plant Cell Physiol. 57(12): 2497–2509 (2016) doi:10.1093/pcp/pcw178 stringent regiospecificity of G4DT for the C-4 position of glyci- Table 1 Predicted genes with high sequence identity to AtVTE2-1 nol. These data suggest that another PT is involved in the bio- from the soybean genome database synthesis of glyceollins II–V (Fig. 1), which should be referred to Sequence ID of Identity of the Full-length Function of as DMAPP:(À)-glycinol 2-dimethylallyltransferase (G2DT). the Phytozome nucleotide and coding the Recent reports also illustrated that elicitor-treated soybeans database (v11.0) deduced amino sequence encoded acid sequence information protein accumulate glyceollins and several prenylated isoflavonoids, (in parentheses) available 0 including 4-dimethylallylcoumestrol, 3 -dimethylallyldaidzein, to AtVTE2-1 (%) using EST data 0 3 -dimethylallylgenistein and 8-dimethylallyldaidzein (Cheng Glyma.13G097800 (PT1) 66 (78) Yes HPTa et al. 2011, Simons et al. 2011) (Fig. 1), further indicating the Glyma.03G033100 54 (55) No – presence of several isoflavonoid PTs with varying substrate spe- Glyma.10G070100 58 (54) No – cificities and regiospecificities in soybean. Glyma.10G070300 57 (49) No – Glyma.11G210500 60 (56) No – The structural diversity of plant specialized metabolites is Glyma.10G295300
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