Shoot branching is a major determinant of plant architecture and is highly regulated by endogenous and environmental cues. Two classes of hormones, auxin and cytokinin, have long been known to have an important involvement in controlling shoot branching. Previous studies using a series of mutants with enhanced shoot branching suggested the existence of a third class of hormone(s) that is derived from carotenoids, but its chemical identity has been unknown. Here we show that levels of strigolactones, a group of terpenoid lactones, are significantly reduced in some of the branching mutants. Furthermore, application of strigolactones inhibits shoot branching in these mutants. Strigolactones were previously found in root exudates acting as communication chemicals with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Thus, we propose that strigolactones act as a new hormone class-or their biosynthetic precursors-in regulating above-ground plant architecture, and also have a function in underground communication with other neighbouring organisms.

The hormonal action of abscisic acid (ABA) in plants is controlled by the precise balance between its biosynthesis and catabolism. In plants, ABA 8 0 -hydroxylation is thought to play a predominant role in ABA catabolism. ABA 8 0 -hydroxylase was shown to be a cytochrome P450 (P450); however, its corresponding gene had not been identified. Through phylogenetic and DNA microarray analyses during seed imbibition, the candidate genes for this enzyme were narrowed down from 272 Arabidopsis P450 genes. These candidate genes were functionally expressed in yeast to reveal that members of the CYP707A family, CYP707A1-CYP707A4, encode ABA 8 0 -hydroxylases. Expression analyses revealed that CYP707A2 is responsible for the rapid decrease in ABA level during seed imbibition. During drought stress conditions, all CYP707A genes were upregulated, and upon rehydration a significant increase in mRNA level was observed. Consistent with the expression analyses, cyp707a2 mutants exhibited hyperdormancy in seeds and accumulated six-fold greater ABA content than wild type. These results demonstrate that CYP707A family genes play a major regulatory role in controlling the level of ABA in plants.

The hormone-mediated control of plant growth and development involves both synthesis and response. Previous studies have shown that gibberellin (GA) plays an essential role in Arabidopsis seed germination. To learn how GA stimulates seed germination, we performed comprehensive analyses of GA biosynthesis and response using gas chromatography-mass spectrometry and oligonucleotide-based DNA microarray analysis. In addition, spatial correlations between GA biosynthesis and response were assessed by in situ hybridization. We identified a number of transcripts, the abundance of which is modulated upon exposure to exogenous GA. A subset of these GA-regulated genes was expressed in accordance with an increase in endogenous active GA levels, which occurs just before radicle emergence. The GA-responsive genes identified include those responsible for synthesis, transport, and signaling of other hormones, suggesting the presence of uncharacterized crosstalk between GA and other hormones. In situ hybridization analysis demonstrated that the expression of GAresponsive genes is not restricted to the predicted site of GA biosynthesis, suggesting that GA itself, or GA signals, is transmitted across different cell types during Arabidopsis seed germination.

The phytohormone auxin plays critical roles in the regulation of plant growth and development. Indole-3-acetic acid (IAA) has been recognized as the major auxin for more than 70 y. Although several pathways have been proposed, how auxin is synthesized in plants is still unclear. Previous genetic and enzymatic studies demonstrated that both TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) flavin monooxygenase-like proteins are required for biosynthesis of IAA during plant development, but these enzymes were placed in two independent pathways. In this article, we demonstrate that the TAA family produces indole-3-pyruvic acid (IPA) and the YUC family functions in the conversion of IPA to IAA in Arabidopsis (Arabidopsis thaliana) by a quantification method of IPA using liquid chromatography-electrospray ionization-tandem MS. We further show that YUC protein expressed in Escherichia coli directly converts IPA to IAA. Indole-3-acetaldehyde is probably not a precursor of IAA in the IPA pathway. Our results indicate that YUC proteins catalyze a rate-limiting step of the IPA pathway, which is the main IAA biosynthesis pathway in Arabidopsis.plant hormone | metabolism

Autophagy is an evolutionarily conserved intracellular process for vacuolar degradation of cytoplasmic components. In higher plants, autophagy defects result in early senescence and excessive immunity-related programmed cell death (PCD) irrespective of nutrient conditions; however, the mechanisms by which cells die in the absence of autophagy have been unclear. Here, we demonstrate a conserved requirement for salicylic acid (SA) signaling for these phenomena in autophagydefective mutants (atg mutants). The atg mutant phenotypes of accelerated PCD in senescence and immunity are SA signaling dependent but do not require intact jasmonic acid or ethylene signaling pathways. Application of an SA agonist induces the senescence/cell death phenotype in SA-deficient atg mutants but not in atg npr1 plants, suggesting that the cell death phenotypes in the atg mutants are dependent on the SA signal transducer NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1. We also show that autophagy is induced by the SA agonist. These findings imply that plant autophagy operates a novel negative feedback loop modulating SA signaling to negatively regulate senescence and immunity-related PCD.

Bioactive gibberellins (GAs) are phytohormones that regulate growth and development throughout the life cycle of plants. DELLA proteins are conserved growth repressors that modulate all aspects of GA responses. These GA-signaling repressors are nuclear localized and likely function as transcriptional regulators. Recent studies demonstrated that GA, upon binding to its receptor, derepresses its signaling pathway by binding directly to DELLA proteins and targeting them for rapid degradation via the ubiquitin-proteasome pathway. Therefore, elucidating the signaling events immediately downstream of DELLA is key to our understanding of how GA controls plant development. Two sets of microarray studies followed by quantitative RT-PCR analysis allowed us to identify 14 early GA-responsive genes that are also early DELLA-responsive in Arabidopsis thaliana seedlings. Chromatin immunoprecipitation provided evidence for in vivo association of DELLA with promoters of eight of these putative DELLA target genes. Expression of all 14 genes was downregulated by GA and upregulated by DELLA. Our study reveals that DELLA proteins play two important roles in GA signaling: (1) they help establish GA homeostasis by direct feedback regulation on the expression of GA biosynthetic and GA receptor genes, and (2) they promote the expression of downstream negative components that are putative transcription factors/regulators or ubiquitin E2/E3 enzymes. In addition, one of the putative DELLA targets, XERICO, promotes accumulation of abscisic acid (ABA) that antagonizes GA effects. Therefore, DELLA may restrict GA-promoted processes by modulating both GA and ABA pathways.

SummaryTo reveal the transcriptomes of Arabidopsis seed, comprehensive expression analysis was performed using ATH1 GeneChips (Affymetrix, Santa Clara, CA, USA). In the dry seed, more than 12 000 stored mRNA species were detected, including all ontological categories. Statistical analysis revealed that promoters of highly expressed genes in wild-type dry seeds overrepresented abscisic acid-responsive elements (ABREs) containing the core motif ACGT. Although the coupling element and seed-specific enhancer RY motif alone were not prominently overrepresented in genes with high expression, the presence of these elements in combination with ABRE was associated with particularly high gene expression. The transcriptome of the imbibed seeds differed from that of the dry seed even at 6 h after seed imbibition. After imbibition many upregulated and downregulated genes were co-regulated in clusters of three to five genes. Genes for which expression was affected by the abi5 mutation tended to be located in clusters, suggesting that transactivation by ABI5 is not restricted to a single gene, but affects other proximal genes. Furthermore, cytosine methylation was observed not only in large silent retrotransposon clusters in centromeric regions, but also in non-centromeric silent gene clusters in the seed. These results suggest that such regions might be transcriptionally silenced by methylation or heterochromatin structures. Our analyses reveal that transcriptomes of Arabidopsis seed are characterized by multiple regulatory mechanisms: epigenetic chromatin structures, chromosomal locations (e.g. co-regulated gene clusters) and cis-acting elements.

Auxin is an essential hormone, but its biosynthetic routes in plants have not been fully defined. In this paper, we show that the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) family of amino transferases converts tryptophan to indole-3-pyruvate (IPA) and that the YUCCA (YUC) family of flavin monooxygenases participates in converting IPA to indole-3-acetic acid, the main auxin in plants. Both the YUCs and the TAAs have been shown to play essential roles in auxin biosynthesis, but it has been suggested that they participate in two independent pathways. Here, we show that all of the taa mutant phenotypes, including defects in shade avoidance, root resistance to ethylene and N-1-naphthylphthalamic acid (NPA), are phenocopied by inactivating YUC genes. On the other hand, we show that the taa mutants in several known auxin mutant backgrounds, including pid and npy1, mimic all of the well-characterized developmental defects caused by combining yuc mutants with the auxin mutants. Furthermore, we show that overexpression of YUC1 partially suppresses the shade avoidance defects of taa1 and the sterile phenotypes of the weak but not the strong taa mutants. In addition, we discovered that the auxin overproduction phenotypes of YUC overexpression lines are dependent on active TAA genes. Our genetic data show that YUC and TAA work in the same pathway and that YUC is downstream of TAA. The yuc mutants accumulate IPA, and the taa mutants are partially IPA-deficient, indicating that TAAs are responsible for converting tryptophan to IPA, whereas YUCs play an important role in converting IPA to indole-3-acetic acid.