Genome-wide analysis of phenylpropanoid defence pathways

Abstract

Phenylpropanoids can function as preformed and inducible antimicrobial compounds, as well as signal molecules, in plant-microbe interactions. Since we last reviewed the field 8 years ago, there has been a huge increase in our understanding of the genes of phenylpropanoid biosynthesis and their regulation, brought about largely by advances in genome technology, from whole-genome sequencing to massively parallel gene expression profiling. Here, we present an overview of the biosynthesis and roles of phenylpropanoids in plant defence, together with an analysis of confirmed and predicted phenylpropanoid pathway genes in the sequenced genomes of 11 plant species. Examples are provided of phylogenetic and expression clustering analyses, and the large body of underlying genomic data is provided through a website accessible from the article.

Figure 1

Basic structures of the phenylpropanoid classes described in this article.

Figure 2

The monolignol biosynthetic pathway. The enzymes are as follows: CAD, cinnamyl alcohol dehydrogenase; CCoAOMT, caffeoyl CoA 3‐O‐methyl transferase; CCR, cinnamoyl CoA reductase; C3H, 4‐coumaroylshikimate 3‐hydroxylase; C4H, cinnamate 4‐hydroxylase; 4CL, 4‐coumarate:CoA ligase; COMT, caffeic acid O‐methyltransferase; DP, dirigent protein; F5H, ferulic acid 5‐hydroxylase; HCT, hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase; LAC, laccase; PAL, l‐phenylalanine ammonia‐lyase; PER, peroxidase; PLR, pinoresinol/lariciresinol reductase; SIRD, secoisolariciresinol dehydrogenase.

Figure 3

Biosynthesis of flavonoids and isoflavonoids. The enzymes are as follows: C4H, cinnamate 4‐hydroxylase; CHI, chalcone isomerase; CHR, chalcone reductase; CHS, chalcone synthase; 4CL, 4‐coumarate:CoA ligase; DMID, 7,2′‐dihydroxy‐4′‐methoxy‐isoflavonol dehydratase; FSII, flavone synthase II; 2HID, 2‐hydroxyisoflavanone dehydratase; HI4′OMT, 2‐hydroxyisoflavanone 4′‐O‐methyltransferase; IFR, isoflavone reductase; IFS, isoflavone synthase; I2′H, isoflavone 2′‐hydroxylase; PAL, l‐phenylalanine ammonia‐lyase; VR, vestitone reductase.

Figure 4

Distribution of chalcone synthase (CHS)‐related genes in multiple sequenced genomes. (A) The number of CHS‐related and true CHS genes in the genomes of 11 species. (B) Size of the genomes of the 11 species in (A). (C) Map positions of CHS‐related genes on chromosomes of Medicago truncatula, Oryza sativa, Arabidopsis thaliana and Glycine max.

Figure 5

Phylogenetic trees of CHS‐related genes (A), aldo‐keto reductases (B) and chalcone isomerases (C). Deduced amino acid sequences were aligned using the L‐INS‐i method (Katoh and Toh, 2008) (the mafft program is available online at http://align.bmr.kyushu‐u.ac.jp/mafft/software/) and subsequently inspected by eye. Neighbour‐joining analyses were performed on the aligned sequences using Geneious v4.7 software (Drummond et al., 2009). The bootstrap replicates were 1000 (support thresholds greater than 50% are given at the nodes). Abbreviations: CHI, chalcone isomerase; CHIL, chalcone isomerase‐like; CHR, chalcone reductase; CHS, chalcone synthase; CHSL, chalcone synthase‐like; STS, stilbene synthase. Genes encoding enzymes from 11 species are colour‐coded as follows: Physcomitrella patens (Pp), light green; Selaginella moellendorffii (Selmo), dark green; Populus trichocarpa (Poptr), grey; Arabidopsis thaliana (At), maroon; Vitis vinifera (Vv), dark violet; Medicago truncatula (Medtr), blue; Lotus japonicus (Lj), cobalt; Glycine max (Glyma), light blue; Oryza sativa (Os), red; Sorghum bicolor (Sorbi), yellow ochre; Zea mays (Zm), orange. Bootstrap values for the nodes of the CHS‐related gene tree (A) are provided in Fig. 2 (see Supporting Information). Protein sequences from the 11 species are available online (http://bioinfo.noble.org/manuscript‐support/mpp/). Gene names from additional different species are colour‐coded in black. Accession numbers for genes encoding enzymes from additional species: for CHSs, Gerbera hybrida cultivar, GerberaCHS1 (P48390), GerberaCHS3 (P48392); Ipomoea purpurea, IpCHSA (P48397), IpCHSB (P48398), IpCHSE (O22047); Petunia hybrida, PetuniaCHSB (P22924), PetuniaCHSD (P22925), PetuniaCHSG (P22927); Arachis hypogaea, AhCHS (AAO32821), AhSTS1 (P20178), AhSTS3 (P51069); Bauhinia variegate, BvSTS (ABF59517); Medicago sativa, MsCHS2 (P30074); Cannabis sativa, CsCHS (AAL92879); Rosa hybrida cultivar, RosaCHS (BAC66467); Rubus idaeus, RiCHS (AAK15174); Sorbus aucuparia, SaCHS (ABB89213); for STSs, Vitis vinifera, VvSTS1 (ABJ97071), VvSTS2 (P51070), VvSTS3 (P51071); for CHRs, Glycyrrhiza echinata, GlecCHR (D83718); Medicago sativa, MsCHR (X82368); Pueraria montana var. lobata PmCHR (AF462632); for CHIs type I, Zea mays (Q08704); Citrus sinensis (BAA36552); Dianthus caryophyllus (Q43754); Elaeagnus umbellate (O65333); Ipomoea purpurea (O22604); Petunia hybrida (AAF60296); Raphanus sativus (O22651); for CHIs type II, Medicago sativa (P28012); Pueraria montana var. lobata (Q43056); Phaseolus vulgaris (P14298).

Figure 6

Putative positions of the substrate recognition sites of CYP93 family enzymes in soybean, Medicago and Lotus. The figure was generated based on the study of Sawada et al., 2002. FSII, flavone synthase II; IFS, isoflavone synthase.

Figure 7

Hierarchical clustering analysis of expression patterns of flavonoid biosynthesis genes in microarray experiments involving exposure of plants to pathogens or pathogen‐derived elicitors. (A) Arabidopsis thaliana; (B) Medicago truncatula. Microarray data were obtained for A. thaliana at AtGenExpress (http://www.weigelworld.org/resources/microarray/AtGenExpress/) and for M. truncatula from MtGEAv2 (http://bioinfo.noble.org/gene‐atlas/v2/). Treatment/control fold‐change values were calculated, converted into a log2 scale (see website online) and subjected to hierarchical cluster analysis (pvclust; Suzuki and Shimodaira, 2006). Clusters with approximately unbiased (AU) P value probability of more than 95% are indicated by the red rectangles. Functionally characterized genes are underlined in blue; their National Center for Biotechnology Information (NCBI) gene accession numbers and primary literature citations are available at http://bioinfo.noble.org/manuscript‐support/mpp/.