Approaching cellular and molecular resolution of auxin biosynthesis and metabolism

Abstract

There is abundant evidence of multiple biosynthesis pathways for the major naturally occurring auxin in plants, indole-3-acetic acid (IAA), and examples of differential use of two general routes of IAA synthesis, namely Trp-dependent and Trp-independent. Although none of these pathways has been completely defined, we now have examples of specific IAA biosynthetic pathways playing a role in developmental processes by way of localized IAA synthesis, causing us to rethink the interactions between IAA synthesis, transport, and signaling. Recent work also points to some IAA biosynthesis pathways being specific to families within the plant kingdom, whereas others appear to be more ubiquitous. An important advance within the past 5 years is our ability to monitor IAA biosynthesis and metabolism at increasingly higher resolution.

Figure 1.

Monitoring de novo IAA synthesis by stable isotope labeling. Live plants readily take up deuterium oxide (²H₂O) from the medium, and deuterium readily exchanges with hydrogens in the course of normal metabolism. In the case of IAA, it has been demonstrated that indole-ring deuteriums will not exchange with hydrogens, even in the presence of strong base (Magnus et al. 1980), so measuring the rate of incorporation of deuterium into IAA over a short time period (typically 24 h) indicates the rate of de novo IAA synthesis, as opposed to the hydrolysis of IAA conjugates. n refers to a variable number of deuteriums, from one to five. (E4P) Erythrose-4-phospate, (PEP) phosphoenol pyruvate, (DAHP) 3-deoxy-D-arabino-heptulosonate 7-phosphate, (DHQ) dehydroquinate, (ANA) anthranilate, (IGP) indole-3-glycerol phosphate, (Trp) tryptophan, (IAA) indole-3-acetic acid.

Figure 2.

Proposed IAA biosynthesis pathways for Arabidopsis. Dashed arrows indicate that neither a gene nor enzyme activity has been identified in Arabidopsis. (ANA) anthranilate, (PANA) 5-phosphoribosylanthranilate, (CADP) 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate, (IGP) indole-3-glycerol phosphate, (TRP) tryptophan, (IAM) indole-3-acetamide, (IPA) indole-3-pyruvic acid, (IAAld) indole-3-acetaldehyde, (IAOx) indole-3-acetaldoxime, (S-IAH-L-cys) S-(indolylacetohydroximoyl)-l-cysteine, (indole-3-T-OH) indole-3-thiohydroximate, (IG) indole-3-methylglucosinolate, (TRM) tryptamine, (IAN) indole-3-acetonitrile, (DHCA) dihydrocamalexic acid. Gene abbreviations are given in upper case italics. Mutant alleles are indicated in lower case italics. In the case of aldehyde oxidase, this enzyme activity has been proposed for the corresponding conversion, but a definitive gene assignment has not been made (Sekimoto et al. 1998; Seo et al. 1998). Arabidopsis encodes at least four myrosinases, TGG1 and TGG2 (Barth and Jander 2006), and two others (reviewed in Halkier and Gershenzon 2006), and at least one epithiospecifier (ESP) locus (Lambrix et al. 2001) and an epithiospecifier modifier (ESM1) gene has been identified (Burow et al. 2008). Mutant phenotypes and references therein for trp2, trp3, cyp79b2cyp79b3, sur1, sur2, and nit 1 are described in Woodward and Bartel 2005 and in Last and Fink 1988 for trp1. Mutants identified since the Woodward and Bartel review include wei2, wei7 (Stepanova et al. 2005), jdl1 (Sun et al. 2009), wei8 (Stepanova et al. 2008), sav3 (Tao et al. 2008), tir2 (Yamada et al. 2009), pad3 (Zhao et al. 1999; Bottcher et al. 2009), and pad4 (Nafisi et al. 2007).

Figure 3.

IAA metabolism in Arabidopsis. Updated from Woodward and Bartel 2005. Genes identified since the Woodward and Bartel review include GS3.2-GS3.6 and GS3.17 (Staswick et al. 2002; Staswick et al. 2005). Recently identified IAA-metabolites include IAA-Leu, IAA-Ala (Kowalczyk and Sandberg 2001; Rampey et al. 2004), IAA-Phe, IAA-Val (Kai et al. 2007a), IAA-Trp (Staswick 2009), oxIAA-Asp, oxIAA-hexose (Ostin et al. 1998), oxIAA-Glu, -Val, -Phe and –glucose (Kai et al. 2007a), 6-OH-IAA-Val and -Phe (Kai et al. 2007a), and methyl-IAA (Qin et al. 2005). IBA is a substrate for some of the GH3 genes, as indicated by in vitro assay (Staswick et al. 2005). See Cohen and Bandurski 1982, Normanly 1997, and Seidel et al. 2006 for IAA metabolites identified in other species. Dashed arrows indicate that the enzyme activity has been observed in vitro only, or neither gene nor enzyme activity have been identified.