How growth regulators provoke context-specific signals is a fundamental question in developmental biology. In plants, both auxin and brassinosteroids (BRs) promote cell expansion, and it was thought that they activated this process through independent mechanisms. In this work, we describe a shared auxin:BR pathway required for seedling growth. Genetic, physiological, and genomic analyses demonstrate that response from one pathway requires the function of the other, and that this interdependence does not act at the level of hormone biosynthetic control. Increased auxin levels saturate the BR-stimulated growth response and greatly reduce BR effects on gene expression. Integration of these two pathways is downstream from BES1 and Aux/IAA proteins, the last known regulatory factors acting downstream of each hormone, and is likely to occur directly on the promoters of auxin:BR target genes. We have developed a new approach to identify potential regulatory elements acting in each hormone pathway, as well as in the shared auxin:BR pathway. We show that one element highly overrepresented in the promoters of auxin- and BR-induced genes is responsive to both hormones and requires BR biosynthesis for normal expression. This work fundamentally alters our view of BR and auxin signaling and describes a powerful new approach to identify regulatory elements required for response to specific stimuli.
References
[1]
Abel S, Nguyen MD, Theologis A (1995) The PS-IAA4/5-like family of early auxin-inducible mRNAs in . J Mol Biol 251: 533–549.
[2]
Alonso JM, Ecker JR (2001) The ethylene pathway: A paradigm for plant hormone signaling and interaction. Sci STKE 2001: RE1.
[3]
Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3: 21–29.
[4]
Bouquin T, Meier C, Foster R, Nielsen ME, Mundy J (2001) Control of specific gene expression by gibberellin and brassinosteroid. Plant Physiol 127: 450–458.
[5]
Clay NK, Nelson T (2002) VH1, a provascular cell-specific receptor kinase that influences leaf cell patterns in Arabidopsis. Plant Cell 14: 2707–2722.
[6]
Clouse S (2002) Brasinosteroids. In: Somerville CR, Meyerowitz EM, editors. The Arabidopsis book. Available: http://www.aspb.org/downloads/arabidopsi?s/clouse.pdf via the Internet. Accessed 8 July 2004.
[7]
Clouse S, Zurek DM, McMorris TC, Baker ME (1992) Effect of brassinolide on gene expression in elongating soybean epicotyls. Plant Physiol 100: 1377–1383.
[8]
Collett CE, Harberd NP, Leyser O (2000) Hormonal interactions in the control of Arabidopsis hypocotyl elongation. Plant Physiol 124: 553–562.
[9]
DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686.
[10]
Friedrichsen DM, Nemhauser J, Muramitsu T, Maloof JN, Alonso J, et al. (2002) Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics 162: 1445–1456.
[11]
Fu X, Harberd NP (2003) Auxin promotes Arabidopsis root growth by modulating gibberellin response. Nature 421: 740–743.
[12]
Ghassemian M, Nambara E, Cutler S, Kawaide H, Kamiya Y, et al. (2000) Regulation of abscisic acid signaling by the ethylene response pathway in Arabidopsis. Plant Cell 12: 1117–1126.
[13]
Ghislain J, Desmarquet-Trin-Dinh C, Gilardi-Hebenstreit P, Charnay P, Frain M (2003) Neural crest patterning: autoregulatory and crest-specific elements co-operate for Krox20 transcriptional control. Development 130: 941–953.
[14]
Goda H, Shimada Y, Asami T, Fujioka S, Yoshida S (2002) Microarray analysis of brassinosteroid-regulated genes in Arabidopsis. Plant Physiol 130: 1319–1334.
[15]
Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, et al. (2004) Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. Plant Physiol 134: 1–19.
[16]
Gray WM, Ostin A, Sandberg G, Romano CP, Estelle M (1998) High temperature promotes auxin-mediated hypocotyl elongation in Arabidopsis. Proc Natl Acad Sci U S A 95: 7197–7202.
[17]
Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M (2001) Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins. Nature 414: 271–276.
[18]
Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, et al. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110–2113.
[19]
He JX, Gendron JM, Yang Y, Li J, Wang ZY (2002) The GSK3-like kinase BIN2 phosphorylates and destabilizes BZR1, a positive regulator of the brassinosteroid signaling pathway in Arabidopsis. Proc Natl Acad Sci U S A 99: 10185–10190.
[20]
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res 27: 297–300.
[21]
Hochberg Y (1988) A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75: 800–802.
[22]
Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comput Graph Stat 5: 299–314.
[23]
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249–264.
[24]
Kang JG, Yun J, Kim DH, Chung KS, Fujioka S, et al. (2001) Light and brassinosteroid signals are integrated via a dark-induced small G protein in etiolated seedling growth. Cell 105: 625–636.
[25]
Kim J, Harter K, Theologis A (1997) Protein-protein interactions among the Aux/IAA proteins. Proc Natl Acad Sci U S A 94: 11786–11791.
[26]
Leyser HM, Pickett FB, Dharmasiri S, Estelle M (1996) Mutations in the AXR3 gene of Arabidopsis result in altered auxin response including ectopic expression from the SAUR-AC1 promoter. Plant J 10: 403–413.
[27]
Li J, Nam KH (2002) Regulation of brassinosteroid signaling by a GSK3/SHAGGY-like kinase. Science 295: 1299–1301.
[28]
Li J, Nagpal P, Vitart V, McMorris TC, Chory J (1996) A role for brassinosteroids in light-dependent development of Arabidopsis. Science 272: 398–401.
[29]
Lincoln C, Britton JH, Estelle M (1990) Growth and development of the axr1 mutants of Arabidopsis. Plant Cell 2: 1071–1080.
[30]
Liscum E, Reed JW (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol Biol 49: 387–400.
[31]
Lorenzo O, Piqueras R, Sanchez-Serrano JJ, Solano R (2003) ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense. Plant Cell 15: 165–178.
[32]
Mandava NB (1988) Plant growth-promoting brassinosteroids. Annu Rev Plant Physiol Plant Mol Biol 39: 23–52.
[33]
Mandava NB, Sasse JM, Yopp JH (1981) Brassinolide, a growth-promoting steroidal lactone I. Activity in selected gibberellin and cytokinin bioassays. Physiol Plantarum 53: 453–461.
[34]
Marchal K, Thijs G, De Keersmaecker S, Monsieurs P, De Moor B, et al. (2003) Genome-specific higher-order background models to improve motif detection. Trends Microbiol 11: 61–66.
[35]
Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D (2004) Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res 32: 949–958.
Nakamura A, Higuchi K, Goda H, Fujiwara MT, Sawa S, et al. (2003a) Brassinolide induces IAA5, IAA19, and DR5, a synthetic auxin response element in Arabidopsis, implying a cross talk point of brassinosteroid and auxin signaling. Plant Physiol 133: 1–11.
[38]
Nakamura A, Shimada Y, Goda H, Fujiwara MT, Asami T, et al. (2003b) AXR1 is involved in BR-mediated elongation and SAUR-AC1 gene expression in Arabidopsis. FEBS Lett 553: 28–32.
[39]
Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, et al. (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34: 137–148.
[40]
Nemhauser JL, Chory J (2002) Photomorphogenesis. In: Somerville CR, Meyerowitz EM, editors. The Arabidopsis book. Available: http://www.aspb.org/downloads/arabidopsi?s/nemhau.pdf via the Internet. Accessed 8 July 2004.
[41]
Nemhauser JL, Maloof JN, Chory J (2003) Building integrated models of plant growth and development. Plant Physiol 132: 436–439.
[42]
Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, et al. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol 132: 1162–1176.
[43]
Ross JJ, O'Neill DP, Smith JJ, Kerckhoffs LH, Elliott RC (2000) Evidence that auxin promotes gibberellin A1 biosynthesis in pea. Plant J 21: 547–552.
[44]
Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16: 939–945.
[45]
Ruegger M, Dewey E, Gray WM, Hobbie L, Turner J, et al. (1998) The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast grr1p. Genes Dev 12: 198–207.
[46]
Sessions A, Weigel D, Yanofsky MF (1999) The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal expression in meristems and young primordia. Plant J 20: 259–263.
[47]
Singh KB (1998) Transcriptional regulation in plants: The importance of combinatorial control. Plant Physiol 118: 1111–1120.
[48]
Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: 3. Available: http://www.bepress.com/sagmb/vol3/iss1/a?rt3/ via the Internet. Accessed 7 July 2004.
[49]
Subramaniam N, Campion J, Rafter I, Okret S (2003) Cross-talk between glucocorticoid and retinoic acid signals involving glucocorticoid receptor interaction with the homoeodomain protein Pbx1. Biochem J 370: 1087–1095.
[50]
Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, et al. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 17: 1113–1122.
[51]
Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, et al. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 9: 447–464.
[52]
Tian Q, Reed J (2001) Molecular links between light and auxin signaling pathways. J Plant Growth Reg 20: 274–280.
[53]
Timpte C, Wilson AK, Estelle M (1994) The axr2–1 mutation of is a gain-of-function mutation that disrupts an early step in auxin response. Genetics 138: 1239–1249.
[54]
Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15: 533–543.
[55]
Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM (2004) Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem 279: 20167–20177.
[56]
Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ (1995) Composite structure of auxin response elements. Plant Cell 7: 1611–1623.
[57]
Ulmasov T, Hagen G, Guilfoyle TJ (1997a) ARF1, a transcription factor that binds to auxin response elements. Science 276: 1865–1868.
[58]
Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ (1997b) Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9: 1963–1971.
[59]
Ulmasov T, Hagen G, Guilfoyle TJ (1999) Dimerization and DNA binding of auxin response factors. Plant J 19: 309–319.
[60]
van Helden J, Andre B, Collado-Vides J (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281: 827–842.
[61]
Vogel JP, Woeste KE, Theologis A, Kieber JJ (1998) Recessive and dominant mutations in the ethylene biosynthetic gene ACS5 of Arabidopsis confer cytokinin insensitivity and ethylene overproduction, respectively. Proc Natl Acad Sci U S A 95: 4766–4771.
[62]
Wang ZY, Seto H, Fujioka S, Yoshida S, Chory J (2001) BRI1 is a critical component of a plasma-membrane receptor for plant steroids. Nature 410: 380–383.
[63]
Yang SF, Hoffman NE (1984) Ethylene biosynthesis and its regulation in higher plants. Annu Rev Plant Phys 35: 155–189.
[64]
Yin Y, Wang ZY, Mora-Garcia S, Li J, Yoshida S, et al. (2002a) BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell 109: 181–191.
[65]
Yin Y, Wu D, Chory J (2002b) Plant receptor kinases: Systemin receptor identified. Proc Natl Acad Sci U S A 99: 9090–9092.
[66]
Zenser N, Dreher KA, Edwards SR, Callis J (2003) Acceleration of Aux/IAA proteolysis is specific for auxin and independent of AXR1. Plant J 35: 285–294.
[67]
Zhao Y, Christensen SK, Fankhauser C, Cashman JR, Cohen JD, et al. (2001) A role for flavin monooxygenase-like enzymes in auxin biosynthesis. Science 291: 306–309.
[68]
Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, et al. (2002) Trp-dependent auxin biosynthesis in Arabidopsis: Involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev 16: 3100–3112.
[69]
Zhao Y, Dai X, Blackwell HE, Schreiber SL, Chory J (2003) SIR1, an upstream component in auxin signaling identified by chemical genetics. Science 301: 1107–1110.
[70]
Zurek DM, Rayle DL, McMorris TC, Clouse SD (1994) Investigation of gene expression, growth kinetics, and wall extensibility during brassinosteroid-regulated stem elongation. Plant Physiol 104: 505–513.