Okushima, Y. et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17, 444-463

Plant Gene Expression Center, Albany, California 94710, USA.
The Plant Cell (Impact Factor: 9.34). 03/2005; 17(2):444-63. DOI: 10.1105/tpc.104.028316
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The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression. The biological function(s) of most ARFs is poorly understood. Here, we report the identification and characterization of T-DNA insertion lines for 18 of the 23 ARF gene family members in Arabidopsis thaliana. Most of the lines fail to show an obvious growth phenotype except of the previously identified arf2/hss, arf3/ett, arf5/mp, and arf7/nph4 mutants, suggesting that there are functional redundancies among the ARF proteins. Subsequently, we generated double mutants. arf7 arf19 has a strong auxin-related phenotype not observed in the arf7 and arf19 single mutants, including severely impaired lateral root formation and abnormal gravitropism in both hypocotyl and root. Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants. For example, the expression of several genes, such as those encoding members of LATERAL ORGAN BOUNDARIES domain proteins and AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE, are disrupted in the double mutant. The data suggest that the ARF7 and ARF19 proteins play essential roles in auxin-mediated plant development by regulating both unique and partially overlapping sets of target genes. These observations provide molecular insight into the unique and overlapping functions of ARF gene family members in Arabidopsis.

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Available from: Kazunari Arima, Oct 04, 2015
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    • "The tir1 mutant was obtained from the Arabidopsis Biological Stock Center. The slr and arf7-1 arf19-1 mutants have been described previously (Fukaki et al. 2002; Okushima et al. 2005; Copyright © 2015 The Japanese Society for Plant Cell and Molecular Biology Okushima et al. 2007). After being sterilized for 15 min with 95% ethanol, seeds were sown on a gellan gum plate ( "
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    ABSTRACT: LAZY1 is a protein involved in gravity signaling of shoot gravitropism of rice, maize and Arabidopsis. Although the lazy1 mutants have been well-characterized, the function of the LAZY1 protein is still largely unknown. In this study, we used fluorescence microscopy to examine the subcellular localization of Arabidopsis LAZY1 (AtLAZY1) and its truncated proteins fused to GFP in tobacco leaves. We found that AtLAZY1 localizes to the plasma membrane through the C-terminal region, suggesting that the putative trans-membrane domain in the N-terminal half is not required for localization. Next, we took a biochemical approach to investigate the membrane association of AtLAZY1. Transiently expressed AtLAZY1 in transgenic Arabidopsis was fractionated in an insoluble fraction that contained membranous compartments. AtLAZY1 was solubilized by a non-ionic detergent or at a high pH condition, suggesting that AtLAZY1 is a peripheral membrane protein. We also found that when expressed in tobacco the C-terminal part of AtLAZY1 co-localized with microtubules. A microtubule binding assay showed that the C-terminal half of AtLAZY1, which localized to the plasma membrane, interacted with microtubules in vitro. These results suggest that AtLAZY1 may function with microtubules at the periphery of the plasma membrane in the gravity signaling process.
    Plant Biotechnology 01/2015; 32(1). DOI:10.5511/plantbiotechnology.15.0116a · 0.87 Impact Factor
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    • "Factors (ARFs) (Okushima et al., 2005) and the Auxin/Indole-3-Acetic Acid (Aux/IAA) genes (Overvoorde et al., 2005), though a nontranscriptional pathway via AUXIN BINDING PROTEIN1 (ABP1) (Sauer and Kleine-Vehn, 2011) has also been identified. A subset of the ARFs are transcription factors that bind target promoters and activate auxin responsive genes, while in contrast the Aux/IAAs dimerise with ARFs and repress transcription (Guilfoyle and Hagen, 2007). "
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    ABSTRACT: Emergence of new lateral roots from within the primary root in Arabidopsis has been shown to be regulated by the phytohormone auxin, via the expression of the auxin influx carrier LAX3, mediated by the ARF7/19 IAA14 signalling module (Swarup et al., 2008). A single cell model of the LAX3 and IAA14 auxin response was formulated and used to demonstrate that hysteresis and bistability may explain the experimentally observed 'all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. The model was tested further by using a parameter fitting algorithm to match model output with qRT-PCR mRNA expression data following exogenous auxin treatment. It was found that the model is able to show good agreement with the data, but only when the exogenous auxin signal is degraded over time, at a rate higher than that measured in the experimental medium, suggesting the triggering of an endogenous auxin homeostasis mechanism. Testing the model over a more physiologically relevant range of extracellular auxin shows bistability and hysteresis still occur when using the optimised parameters, providing the rate of LAX3 active auxin transport is sufficiently high relative to passive diffusion. Copyright © 2014. Published by Elsevier Ltd.
    Journal of Theoretical Biology 11/2014; 366. DOI:10.1016/j.jtbi.2014.11.003 · 2.12 Impact Factor
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    • "As a transcriptional regulator, LBD16 may also activate the downstream transcriptional network for lateral root (LR) initiation (Okushima et al. 2007). The lists of auxinregulated genes of which expression is inhibited in the mutants contain putative downstream targets of ARF7 and ARF19 (Okushima et al. 2005b). "
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    ABSTRACT: Jatropha curcas is a new promising bioenergy crop due to the high oil content in its seeds that can be converted into biodiesel. Seed size, a major determinant of Jatropha oil yield, is a target trait for Jatropha breeding. Due to the vital roles of phytohormone auxin in controlling seed and fruit development, we screened key genes in auxin pathway including ARF and IAA families and downstream effectors to identify candidate genes controlling seed size in Jatropha. As a result, JcARF19 was mapped in the major quantitative trait locus (QTL) region and significantly associated with seed length. By using expression QTL (eQTL) analysis to link variants with functional candidate genes, we provided evidences that seed traits were affected by the interaction of JcARF19 and JcIAA9. ARF19 and IAA9, involved in auxin signal transduction, were conserved in higher plants. These data including the single-nucleotide polymorphisms (SNPs) in the two genes could lead to utilization of the genes by integrating favored alleles into elite varieties through marker-assisted selection.
    Functional & Integrative Genomics 09/2014; 14(4). DOI:10.1007/s10142-014-0400-5 · 2.48 Impact Factor
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