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.2013 Mar 27:4:62.
doi: 10.3389/fpls.2013.00062. eCollection 2013.

Shikimate and phenylalanine biosynthesis in the green lineage

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Shikimate and phenylalanine biosynthesis in the green lineage

Takayuki Tohge et al. Front Plant Sci..

Abstract

The shikimate pathway provides carbon skeletons for the aromatic amino acids l-tryptophan, l-phenylalanine, and l-tyrosine. It is a high flux bearing pathway and it has been estimated that greater than 30% of all fixed carbon is directed through this pathway. These combined pathways have been subjected to considerable research attention due to the fact that mammals are unable to synthesize these amino acids and the fact that one of the enzymes of the shikimate pathway is a very effective herbicide target. However, in addition to these characteristics these pathways additionally provide important precursors for a wide range of important secondary metabolites including chlorogenic acid, alkaloids, glucosinolates, auxin, tannins, suberin, lignin and lignan, tocopherols, and betalains. Here we review the shikimate pathway of the green lineage and compare and contrast its evolution and ubiquity with that of the more specialized phenylpropanoid metabolism which this essential pathway fuels.

Keywords: aromatic amino biosynthesis; evolution; gene copy number; gene duplication; plant secondary phenolic metabolite; shikimate pathway.

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Figures

Figure 1
Figure 1
The shikimate andphenylalanine derived secondary metabolite biosynthesis in plants.(A) Shikimate biosynthesis starting from phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate is described with characterized genes and reported intermediate metabolites.(B) phenylalanine derived major phenolic secondary mebolite biosynthesis in the green lineage. Arrow indicates enzymatic reaction, circle indicates metabolite. Abbreviation: DAHPS, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase; DQS, 3-dehydroquinate synthase; DHQD/SD, 3-dehydroquinate dehydratase; SK, shikimate kinase; ESPS, 3-phosphoshikimate 1-carboxyvinyltransferase; CS, chorismate synthase; CM, chorismate mutase; PAT, prephenate aminotransferase; ADT, arogenate dehydratase. PAL, phenylalanine ammonia-lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumarate CoA ligase; CAD, cinnamoyl-alcohol dehydrogenase; F5H, ferulate 5-hydroxylase; C3H, coumarate 3-hydroxylase; ALDH, aldehyde dehydrogenase; CCR, cinnamoyl-CoA reductase; HCT, hydroxycinnamoyl-Coenzyme A shikimate/quinate hydroxycinnamoyltransferase; CCoAOMT, caffeoyl/CoA-3-O-metheltransferase; CHS, chalcone synthese; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3′H, flavonoid-3′-hydroxylase; F3GT, flavonoid-3-O-glycosyltransferase; FS, flavone synthase; FOMT, flavonoidO-methyltransferase; FCGT, flavone-C-glycosyltransferase; FLS, flavonol synthese; F3GT, flavonoid-3-O-glycosyltransferase; DFR, dihydroflavonol reductase; ANS, Anthocyanidin synthese; AGT, Flavonoid-O-glycosyltransferase; AAT, anthocyanin acyltransferase; BAN, oxidoreductase|dihydroflavonol reductase like; LAC, laccase.
Figure 2
Figure 2
Phylogenetic tree analysis of shikimate and phenylalanine biosynthetic genes in 25 species. Amino acid sequence phylogenetic trees of(A) shikimate pathway: (a), DAHPS, (b) DHS, (c) DHQD/SD, (d) SK, (e) ESPS, and (f) CS,(B) phenylalanine related genes, (a) CM and (b) PAT. Amino acid sequences of shikimate biosynthetic genes are obtained from Plaza database (http://bioinformatics.psb.ugent.be/plaza/). Relationships among the species considered are presented on the Plaza website. The phylogenetic tree was constructed with the aligned protein sequences by MEGA (version 5.10;http://www.megasoftware.net/; Kumar et al., 2004) using the neighbor-joining method with the following parameters: Poisson correction, complete deletion, and bootstrap (1000 replicates, random seed). The protein sequences were aligned by Plaza. Values on the branches indicate bootstrap support in percentages.
Figure 2
Figure 2
Phylogenetic tree analysis of shikimate and phenylalanine biosynthetic genes in 25 species. Amino acid sequence phylogenetic trees of(A) shikimate pathway: (a), DAHPS, (b) DHS, (c) DHQD/SD, (d) SK, (e) ESPS, and (f) CS,(B) phenylalanine related genes, (a) CM and (b) PAT. Amino acid sequences of shikimate biosynthetic genes are obtained from Plaza database (http://bioinformatics.psb.ugent.be/plaza/). Relationships among the species considered are presented on the Plaza website. The phylogenetic tree was constructed with the aligned protein sequences by MEGA (version 5.10;http://www.megasoftware.net/; Kumar et al., 2004) using the neighbor-joining method with the following parameters: Poisson correction, complete deletion, and bootstrap (1000 replicates, random seed). The protein sequences were aligned by Plaza. Values on the branches indicate bootstrap support in percentages.
Figure 3
Figure 3
Heat map for isoforms of shikimate-phenylalanine biosynthetic genes in plant genomes and hypothetical scheme for the evolution of phenylalanine derived phenolic secondary metabolism. (A) Heap map overview of number of shikimate-phenylalanine biosynthetic gene isoforms in 25 species.(B) Hypothetical schematic figure for shikimate-phenylalanine biosynthetic genes and their evolution of phenolic secondary metabolism.
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