1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Plant Biology
  4. Volume 67, 2016
  5. Article

Annual Review of Plant Biology

Volume 67, 2016

Transcriptional Responses to the Auxin Hormone

Abstract

Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.

Keyword(s): ARF, auxin, chromatin, development, gene expression, specificity
Loading

Article metrics loading...

/content/journals/10.1146/annurev-arplant-043015-112122
2016-04-29
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/arplant/67/1/annurev-arplant-043015-112122.html?itemId=/content/journals/10.1146/annurev-arplant-043015-112122&mimeType=html&fmt=ahah

Literature Cited

  1. Abel S, Nguyen MD, Theologis A. 1.  1995. The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J. Mol. Biol. 251:533–49 [Google Scholar]
  2. Abel S, Oeller PW, Theologis A. 2.  1994. Early auxin-induced genes encode short-lived nuclear proteins. PNAS 91:326–30 [Google Scholar]
  3. Allen E, Xie Z, Gustafson AM, Carrington JC. 3.  2005. MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–21 [Google Scholar]
  4. Ashton NW, Grimsley NH, Cove DJ. 4.  1979. Analysis of gametophytic development in the moss, Physcomitrella patens, using auxin and cytokinin resistant mutants. Planta 144:427–35 [Google Scholar]
  5. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M. 5.  et al. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960–63 [Google Scholar]
  6. Barbier de Reuille P, Bohn-Courseau I, Ljung K, Morin H, Carraro N. 6.  et al. 2006. Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis. PNAS 103:1627–32 [Google Scholar]
  7. Bargmann BO, Vanneste S, Krouk G, Nawy T, Efroni I. 7.  et al. 2013. A map of cell type-specific auxin responses. Mol. Syst. Biol. 9:688 [Google Scholar]
  8. Barton MK. 8.  2010. Twenty years on: the inner workings of the shoot apical meristem, a developmental dynamo. Dev. Biol. 341:95–113 [Google Scholar]
  9. Bartrina I, Otto E, Strnad M, Werner T, Schmülling T. 9.  2011. Cytokinin regulates the activity of reproductive meristems, flower organ size, ovule formation, and thus seed yield in Arabidopsis thaliana. Plant Cell 23:69–80 [Google Scholar]
  10. Bates GW, Goldsmith MH. 10.  1983. Rapid response of the plasma-membrane potential in oat coleoptiles to auxin and other weak acids. Planta 159:231–37 [Google Scholar]
  11. Benjamins R, Quint A, Weijers D, Hooykaas P, Offringa R. 11.  2001. The PINOID protein kinase regulates organ development in Arabidopsis by enhancing polar auxin transport. Development 128:4057–67 [Google Scholar]
  12. Bennett SRM, Alvarez J, Bossinger G, Smyth DR. 12.  1995. Morphogenesis in pinoid mutants of Arabidopsis thaliana. Plant J. 8:505–20 [Google Scholar]
  13. Berendzen KW, Weiste C, Wanke D, Kilian J, Harter K, Droge-Laser W. 13.  2012. Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription. BMC Plant Biol. 12:125 [Google Scholar]
  14. Berleth T, Jürgens G. 14.  1993. The role of the monopteros gene in organising the basal body region of the Arabidopsis embryo. Development 118:575–87 [Google Scholar]
  15. Besnard F, Refahi Y, Morin V, Marteaux B, Brunoud G. 15.  et al. 2014. Cytokinin signalling inhibitory fields provide robustness to phyllotaxis. Nature 505:417–21 [Google Scholar]
  16. Blazquez MA, Weigel D. 16.  2000. Integration of floral inductive signals in Arabidopsis. Nature 404:889–92 [Google Scholar]
  17. Boer DR, Freire-Rios A, van den Berg WA, Saaki T, Manfield IW. 17.  et al. 2014. Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 156:577–89 [Google Scholar]
  18. Bowman JL, Floyd SK, Sakakibara K. 18.  2007. Green genes—comparative genomics of the green branch of life. Cell 129:229–34 [Google Scholar]
  19. Braun N, Wyrzykowska J, Muller P, David K, Couch D. 19.  et al. 2008. Conditional repression of AUXIN BINDING PROTEIN1 reveals that it coordinates cell division and cell expansion during postembryonic shoot development in Arabidopsis and tobacco. Plant Cell 20:2746–62 [Google Scholar]
  20. Brunoud G, Wells DM, Oliva M, Larrieu A, Mirabet V. 20.  et al. 2012. A novel sensor to map auxin response and distribution at high spatio-temporal resolution. Nature 482:103–6 [Google Scholar]
  21. Calderon-Villalobos LI, Lee S, De Oliveira C, Ivetac A, Brandt W. 21.  et al. 2012. A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin. Nat. Chem. Biol. 8:477–85 [Google Scholar]
  22. Casimiro I, Marchant A, Bhalerao RP, Beeckman T, Dhooge S. 22.  et al. 2001. Auxin transport promotes Arabidopsis lateral root initiation. Plant Cell 13:843–52 [Google Scholar]
  23. Causier B, Ashworth M, Guo W, Davies B. 23.  2012. The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiol. 158:423–38 [Google Scholar]
  24. Chen G, Fernandez J, Mische S, Courey AJ. 24.  1999. A functional interaction between the histone deacetylase Rpd3 and the corepressor groucho in Drosophila development. Genes Dev. 13:2218–30 [Google Scholar]
  25. Chen JG, Ullah H, Young JC, Sussman MR, Jones AM. 25.  2001. ABP1 is required for organized cell elongation and division in Arabidopsis embryogenesis. Genes Dev. 15:902–11 [Google Scholar]
  26. Chen X, Grandont L, Li H, Hauschild R, Paque S. 26.  et al. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature 516:90–93 [Google Scholar]
  27. Chen Z, Agnew JL, Cohen JD, He P, Shan L. 27.  et al. 2007. Pseudomonas syringae type III effector AvrRpt2 alters Arabidopsis thaliana auxin physiology. PNAS 104:20131–36 [Google Scholar]
  28. Cheng Y, Dai X, Zhao Y. 28.  2006. Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. Genes Dev. 20:1790–99 [Google Scholar]
  29. Cheng Y, Dai X, Zhao Y. 29.  2007. Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis. Plant Cell 19:2430–39 [Google Scholar]
  30. Cheng ZJ, Wang L, Sun W, Zhang Y, Zhou C. 30.  et al. 2013. Pattern of auxin and cytokinin responses for shoot meristem induction results from the regulation of cytokinin biosynthesis by AUXIN RESPONSE FACTOR3. Plant Physiol. 161:240–51 [Google Scholar]
  31. Cho H, Ryu H, Rho S, Hill K, Smith S. 31.  et al. 2014. A secreted peptide acts on BIN2-mediated phosphorylation of ARFs to potentiate auxin response during lateral root development. Nat. Cell Biol. 16:66–76 [Google Scholar]
  32. Christensen SK, Dagenais N, Chory J, Weigel D. 32.  2000. Regulation of auxin response by the protein kinase PINOID. Cell 100:469–78 [Google Scholar]
  33. Clapier CR, Cairns BR. 33.  2009. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78:273–304 [Google Scholar]
  34. Cohen M, Briscoe J, Blassberg R. 34.  2013. Morphogen interpretation: the transcriptional logic of neural tube patterning. Curr. Opin. Genet. Dev. 23:423–28 [Google Scholar]
  35. Cole M, Chandler J, Weijers D, Jacobs B, Comelli P, Werr W. 35.  2009. DORNRÖSCHEN is a direct target of the auxin response factor MONOPTEROS in the Arabidopsis embryo. Development 136:1643–51 [Google Scholar]
  36. Colon-Carmona A, Chen DL, Yeh KC, Abel S. 36.  2000. Aux/IAA proteins are phosphorylated by phytochrome in vitro. Plant Physiol. 124:1728–38 [Google Scholar]
  37. Crawford BC, Sewell J, Golembeski G, Roshan C, Long JA, Yanofsky MF. 37.  2015. Genetic control of distal stem cell fate within root and embryonic meristems. Science 347:655–59 [Google Scholar]
  38. Crawford BC, Yanofsky MF. 38.  2011. HALF FILLED promotes reproductive tract development and fertilization efficiency in Arabidopsis thaliana. Development 138:2999–3009 [Google Scholar]
  39. Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N. 39.  et al. 2015. Low affinity binding site clusters confer Hox specificity and regulatory robustness. Cell 160:191–203 [Google Scholar]
  40. Cui F, Wu S, Sun W, Coaker G, Kunkel B. 40.  et al. 2013. The Pseudomonas syringae type III effector AvrRpt2 promotes pathogen virulence via stimulating Arabidopsis auxin/indole acetic acid protein turnover. Plant Physiol. 162:1018–29 [Google Scholar]
  41. De Rybel B, Adibi M, Breda AS, Wendrich JR, Smit ME. 41.  et al. 2014. Integration of growth and patterning during vascular tissue formation in Arabidopsis. Science 345:1255215 [Google Scholar]
  42. De Rybel B, Möller B, Yoshida S, Grabowicz I, Barbier de Reuille P. 42.  et al. 2013. A bHLH complex controls embryonic vascular tissue establishment and indeterminate growth in Arabidopsis. Dev. Cell 24:426–37 [Google Scholar]
  43. De Smet I, Lau S, Voss U, Vanneste S, Benjamins R. 43.  et al. 2010. Bimodular auxin response controls organogenesis in Arabidopsis. PNAS 107:2705–10 [Google Scholar]
  44. De Smet I, Voss U, Lau S, Wilson M, Shao N. 44.  et al. 2011. Unraveling the evolution of auxin signaling. Plant Physiol. 155:209–21 [Google Scholar]
  45. Depuydt S, Hardtke CS. 45.  2011. Hormone signalling crosstalk in plant growth regulation. Curr. Biol. 21:R365–73 [Google Scholar]
  46. Dharmasiri N, Dharmasiri S, Estelle M. 46.  2005. The F-box protein TIR1 is an auxin receptor. Nature 435:441–45 [Google Scholar]
  47. Dharmasiri N, Dharmasiri S, Jones AM, Estelle M. 47.  2003. Auxin action in a cell-free system. Curr. Biol. 13:1418–22 [Google Scholar]
  48. Dharmasiri N, Dharmasiri S, Weijers D, Karunarathna N, Jurgens G, Estelle M. 48.  2007. AXL and AXR1 have redundant functions in RUB conjugation and growth and development in Arabidopsis. Plant J. 52:114–23 [Google Scholar]
  49. Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M. 49.  et al. 2005. Plant development is regulated by a family of auxin receptor F box proteins. Dev. Cell 9:109–19 [Google Scholar]
  50. Dinesh DC, Kovermann M, Gopalswamy M, Hellmuth A, Calderon-Villalobos LI. 50.  et al. 2015. Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response. PNAS 112:6230–35 [Google Scholar]
  51. Donner TJ, Sherr I, Scarpella E. 51.  2009. Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves. Development 136:3235–46 [Google Scholar]
  52. Dreher KA, Brown J, Saw RE, Callis J. 52.  2006. The Arabidopsis Aux/IAA protein family has diversified in degradation and auxin responsiveness. Plant Cell 18:699–714 [Google Scholar]
  53. Eberharter A, Becker PB. 53.  2002. Histone acetylation: a switch between repressive and permissive chromatin. EMBO Rep. 3:224–29 [Google Scholar]
  54. Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ. 54.  et al. 1996. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell 8:155–68 [Google Scholar]
  55. Enders TA, Oh S, Yang Z, Montgomery BL, Strader LC. 55.  2015. Genome sequencing of Arabidopsis abp1-5 reveals second-site mutations that may affect phenotypes. Plant Cell 27:1820–26 [Google Scholar]
  56. Eshed Y, Baum SF, Bowman JL. 56.  1999. Distinct mechanisms promote polarity establishment in carpels of Arabidopsis. Cell 99:199–209 [Google Scholar]
  57. Farcot E, Lavedrine C, Vernoux T. 57.  2015. A modular analysis of the auxin signalling network. PLOS ONE 10:e0122231 [Google Scholar]
  58. Finet C, Berne-Dedieu A, Scutt CP, Marletaz F. 58.  2013. Evolution of the ARF gene family in land plants: old domains, new tricks. Mol. Biol. Evol. 30:45–56 [Google Scholar]
  59. Flores-Sandoval E, Dierschke T, Fisher TJ, Bowman JL. 59.  2015. Efficient and inducible use of artificial microRNAs in Marchantia polymorpha. Plant Cell Physiol. 57281–90
  60. Flores-Sandoval E, Eklund DM, Bowman JL. 60.  2015. A simple auxin transcriptional response system regulates multiple morphogenetic processes in the liverwort Marchantia polymorpha. PLOS Genet. 11:e1005207 [Google Scholar]
  61. Franco-Zorrilla JM, Lopez-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 61.  2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. PNAS 111:2367–72 [Google Scholar]
  62. Friml J, Vieten A, Sauer M, Weijers D, Schwarz H. 62.  et al. 2003. Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis. Nature 426:147–53 [Google Scholar]
  63. Friml J, Yang X, Michniewicz M, Weijers D, Quint A. 63.  et al. 2004. A PINOID-dependent binary switch in apical-basal PIN polar targeting directs auxin efflux. Science 306:862–65 [Google Scholar]
  64. Fukaki H, Tameda S, Masuda H, Tasaka M. 64.  2002. Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 gene of Arabidopsis. Plant J. 29:153–68 [Google Scholar]
  65. Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L. 65.  et al. 2013. An integrative model of the control of ovule primordia formation. Plant J. 76:446–55 [Google Scholar]
  66. Gao Y, Zhang Y, Zhang D, Dai X, Estelle M, Zhao Y. 66.  2015. Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development. PNAS 112:2275–80 [Google Scholar]
  67. Gilkerson J, Hu J, Brown J, Jones A, Sun TP, Callis J. 67.  2009. Isolation and characterization of cul1-7, a recessive allele of CULLIN1 that disrupts SCF function at the C terminus of CUL1 in Arabidopsis thaliana. Genetics 181:945–63 [Google Scholar]
  68. Gilkerson J, Kelley DR, Tam R, Estelle M, Callis J. 68.  2015. Lysine residues are not required for proteasome-mediated proteolysis of the auxin/indole acidic acid protein IAA1. Plant Physiol. 168:708–20 [Google Scholar]
  69. Girin T, Paicu T, Stephenson P, Fuentes S, Korner E. 69.  et al. 2011. INDEHISCENT and SPATULA interact to specify carpel and valve margin tissue and thus promote seed dispersal in Arabidopsis. Plant Cell 23:3641–53 [Google Scholar]
  70. Gray WM, del Pozo JC, Walker L, Hobbie L, Risseeuw E. 70.  et al. 1999. Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana. Genes Dev. 13:1678–91 [Google Scholar]
  71. Gray WM, Hellmann H, Dharmasiri S, Estelle M. 71.  2002. Role of the Arabidopsis RING-H2 protein RBX1 in RUB modification and SCF function. Plant Cell 14:2137–44 [Google Scholar]
  72. Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M. 72.  2001. Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature 414:271–76 [Google Scholar]
  73. Gremski K, Ditta G, Yanofsky MF. 73.  2007. The HECATE genes regulate female reproductive tract development in Arabidopsis thaliana. Development 134:3593–601 [Google Scholar]
  74. Grunewald W, De Smet I, De Rybel B, Robert HS, van de Cotte B. 74.  et al. 2013. Tightly controlled WRKY23 expression mediates Arabidopsis embryo development. EMBO Rep. 14:1136–42 [Google Scholar]
  75. Guilfoyle TJ. 75.  2015. The PB1 domain in auxin response factor and Aux/IAA proteins: a versatile protein interaction module in the auxin response. Plant Cell 27:33–43 [Google Scholar]
  76. Guseman JM, Hellmuth A, Lanctot A, Feldman TP, Moss BL. 76.  et al. 2015. Auxin-induced degradation dynamics set the pace for lateral root development. Development 142:905–9 [Google Scholar]
  77. Hadfi K, Speth V, Neuhaus G. 77.  1998. Auxin-induced developmental patterns in Brassica juncea embryos. Development 125:879–87 [Google Scholar]
  78. Hamann T, Benkova E, Baurle I, Kientz M, Jurgens G. 78.  2002. The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS-mediated embryo patterning. Genes Dev. 16:1610–15 [Google Scholar]
  79. Hamann T, Mayer U, Jurgens G. 79.  1999. The auxin-insensitive bodenlos mutation affects primary root formation and apical-basal patterning in the Arabidopsis embryo. Development 126:1387–95 [Google Scholar]
  80. Hardtke CS, Berleth T. 80.  1998. The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J. 17:1405–11 [Google Scholar]
  81. Hardtke CS, Ckurshumova W, Vidaurre DP, Singh SA, Stamatiou G. 81.  et al. 2004. Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4. Development 131:1089–100 [Google Scholar]
  82. Havens KA, Guseman JM, Jang SS, Pierre-Jerome E, Bolten N. 82.  et al. 2012. A synthetic approach reveals extensive tunability of auxin signaling. Plant Physiol. 160:135–42 [Google Scholar]
  83. Hawkins C, Liu Z. 83.  2014. A model for an early role of auxin in Arabidopsis gynoecium morphogenesis. Front. Plant Sci. 5:327 [Google Scholar]
  84. Heisler MG, Atkinson A, Bylstra YH, Walsh R, Smyth DR. 84.  2001. SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein. Development 128:1089–98 [Google Scholar]
  85. Heisler MG, Ohno C, Das P, Sieber P, Reddy GV. 85.  et al. 2005. Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem. Curr. Biol. 15:1899–911 [Google Scholar]
  86. Hellmann H, Hobbie L, Chapman A, Dharmasiri S, Dharmasiri N. 86.  et al. 2003. Arabidopsis AXR6 encodes CUL1 implicating SCF E3 ligases in auxin regulation of embryogenesis. EMBO J. 22:3314–25 [Google Scholar]
  87. Hobbie L, McGovern M, Hurwitz LR, Pierro A, Liu NY. 87.  et al. 2000. The axr6 mutants of Arabidopsis thaliana define a gene involved in auxin response and early development. Development 127:23–32 [Google Scholar]
  88. Holland AJ, Fachinetti D, Han JS, Cleveland DW. 88.  2012. Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells. PNAS 109:E3350–57 [Google Scholar]
  89. Iglesias MJ, Terrile MC, Windels D, Lombardo MC, Bartoli CG. 89.  et al. 2014. MiR393 regulation of auxin signaling and redox-related components during acclimation to salinity in Arabidopsis. PLOS ONE 9e107678
  90. Ishida T, Aida M, Takada S, Tasaka M. 90.  2000. Involvement of CUP-SHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana. Plant Cell Physiol. 41:60–67 [Google Scholar]
  91. Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP. 91.  2006. Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct. Integr. Genom. 6:47–59 [Google Scholar]
  92. Jones AM, Herman EM. 92.  1993. KDEL-containing auxin-binding protein is secreted to the plasma membrane and cell wall. Plant Physiol. 101:595–606 [Google Scholar]
  93. Jonsson H, Heisler MG, Shapiro BE, Meyerowitz EM, Mjolsness E. 93.  2006. An auxin-driven polarized transport model for phyllotaxis. PNAS 103:1633–38 [Google Scholar]
  94. Kalluri UC, Difazio SP, Brunner AM, Tuskan GA. 94.  2007. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol. 7:59 [Google Scholar]
  95. Kato H, Ishizaki K, Kouno M, Shirakawa M, Bowman JL. 95.  et al. 2015. Auxin-mediated transcriptional system with a minimal set of components is critical for morphogenesis through the life cycle in Marchantia polymorpha. PLOS Genet. 11:e1005084 [Google Scholar]
  96. Ke J, Ma H, Gu X, Thelen A, Brunzelle JS. 96.  et al. 2015. Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors. Sci. Adv. 1:E1500107 [Google Scholar]
  97. Keilwagen J, Grau J, Paponov IA, Posch S, Strickert M, Grosse I. 97.  2011. De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLOS Comput. Biol. 7:e1001070 [Google Scholar]
  98. Konishi M, Donner TJ, Scarpella E, Yanagisawa S. 98.  2015. MONOPTEROS directly activates the auxin-inducible promoter of the Dof5.8 transcription factor gene in Arabidopsis thaliana leaf provascular cells. J. Exp. Bot. 66:283–91 [Google Scholar]
  99. Konishi M, Yanagisawa S. 99.  2015. Transcriptional repression caused by Dof5.8 is involved in proper vein network formation in Arabidopsis thaliana leaves. J. Plant Res. 128:643–52 [Google Scholar]
  100. Korasick DA, Westfall CS, Lee SG, Nanao MH, Dumas R. 100.  et al. 2014. Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression. PNAS 111:5427–32 [Google Scholar]
  101. Krogan NT, Berleth T. 101.  2015. The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal. Behav. 10:e992748 [Google Scholar]
  102. Krogan NT, Hogan K, Long JA. 102.  2012. APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19. Development 139:4180–90 [Google Scholar]
  103. Larsson E, Franks RG, Sundberg E. 103.  2013. Auxin and the Arabidopsis thaliana gynoecium. J. Exp. Bot. 64:2619–27 [Google Scholar]
  104. Leblanc N, David K, Grosclaude J, Pradier JM, Barbier-Brygoo H. 104.  et al. 1999. A novel immunological approach establishes that the auxin-binding protein, Nt-abp1, is an element involved in auxin signaling at the plasma membrane. J. Biol. Chem. 274:28314–20 [Google Scholar]
  105. Li H, Ilin S, Wang W, Duncan EM, Wysocka J. 105.  et al. 2006. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442:91–95 [Google Scholar]
  106. Li W, Zhou Y, Liu X, Yu P, Cohen JD, Meyerowitz EM. 106.  2013. LEAFY controls auxin response pathways in floral primordium formation. Sci. Signal. 6:ra23cr [Google Scholar]
  107. Liao CY, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 107.  2015. Reporters for sensitive and quantitative measurement of auxin response. Nat. Methods 12:207–10 [Google Scholar]
  108. Liu C, Xu Z, Chua NH. 108.  1993. Auxin polar transport is essential for the establishment of bilateral symmetry during early plant embryogenesis. Plant Cell 5:621–30 [Google Scholar]
  109. Liu N, Wu S, Van Houten J, Wang Y, Ding B. 109.  et al. 2014. Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. J. Exp. Bot. 65:2507–20 [Google Scholar]
  110. Liu X, Dinh TT, Li D, Shi B, Li Y. 110.  et al. 2014. AUXIN RESPONSE FACTOR 3 integrates the functions of AGAMOUS and APETALA2 in floral meristem determinacy. Plant J. 80:629–41 [Google Scholar]
  111. Liu X, Gao L, Dinh TT, Shi T, Li D. 111.  et al. 2014. DNA topoisomerase I affects Polycomb Group protein-mediated epigenetic regulation and plant development by altering nucleosome distribution in Arabidopsis. Plant Cell 26:2803–17 [Google Scholar]
  112. Liu X, Kim YJ, Muller R, Yumul RE, Liu C. 112.  et al. 2011. AGAMOUS terminates floral stem cell maintenance in Arabidopsis by directly repressing WUSCHEL through recruitment of Polycomb Group proteins. Plant Cell 23:3654–70 [Google Scholar]
  113. Liu Z, Kumari S, Zhang L, Zheng Y, Ware D. 113.  2012. Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PLOS ONE 7:e39786 [Google Scholar]
  114. Liu ZB, Ulmasov T, Shi X, Hagen G, Guilfoyle TJ. 114.  1994. Soybean GH3 promoter contains multiple auxin-inducible elements. Plant Cell 6:645–57 [Google Scholar]
  115. Lohmann D, Stacey N, Breuninger H, Jikumaru Y, Muller D. 115.  et al. 2010. SLOW MOTION is required for within-plant auxin homeostasis and normal timing of lateral organ initiation at the shoot meristem in Arabidopsis. Plant Cell 22:335–48 [Google Scholar]
  116. Long JA, Ohno C, Smith ZR, Meyerowitz EM. 116.  2006. TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312:1520–23 [Google Scholar]
  117. Malamy JE, Benfey PN. 117.  1997. Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124:33–44 [Google Scholar]
  118. Maraschin FDS, Memelink J, Offringa R. 118.  2009. Auxin-induced, SCFTIR1-mediated poly-ubiquitination marks AUX/IAA proteins for degradation. Plant J. 59:100–9 [Google Scholar]
  119. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D. 119.  et al. 2010. miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 22:1104–17 [Google Scholar]
  120. Melnyk CW, Schuster C, Leyser O, Meyerowitz EM. 120.  2015. A developmental framework for graft formation and vascular reconnection in Arabidopsis thaliana. Curr. Biol. 25:1306–18 [Google Scholar]
  121. Mendoza-Soto AB, Sanchez F, Hernandez G. 121.  2012. MicroRNAs as regulators in plant metal toxicity response. Front. Plant Sci. 3:105 [Google Scholar]
  122. Mironova VV, Omelyanchuk NA, Wiebe DS, Levitsky VG. 122.  2014. Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome. BMC Genom. 15:Suppl. 12S4 [Google Scholar]
  123. Möller B, Weijers D. 123.  2009. Auxin control of embryo patterning. Cold Spring Harb. Perspect. Biol. 1a001545
  124. Moon J, Zhao Y, Dai X, Zhang W, Gray WM. 124.  et al. 2007. A new CULLIN 1 mutant has altered responses to hormones and light in Arabidopsis. Plant Physiol. 143:684–96 [Google Scholar]
  125. Moss BL, Mao H, Guseman JM, Hinds TR, Hellmuth A. 125.  et al. 2015. Rate motifs tune auxin/indole-3-acetic acid degradation dynamics. Plant Physiol. 169:803–13 [Google Scholar]
  126. Moubayidin L, Ostergaard L. 126.  2014. Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development. Curr. Biol. 24:2743–48 [Google Scholar]
  127. Muller B, Sheen J. 127.  2008. Cytokinin and auxin interaction in root stem-cell specification during early embryogenesis. Nature 453:1094–97 [Google Scholar]
  128. Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS. 128.  et al. 2005. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 132:4107–18 [Google Scholar]
  129. Nanao MH, Vinos-Poyo T, Brunoud G, Thevenon E, Mazzoleni M. 129.  et al. 2014. Structural basis for oligomerization of auxin transcriptional regulators. Nat. Commun. 5:3617 [Google Scholar]
  130. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N. 130.  et al. 2006. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312:436–39 [Google Scholar]
  131. Nemhauser JL, Feldman LJ, Zambryski PC. 131.  2000. Auxin and ETTIN in Arabidopsis gynoecium morphogenesis. Development 127:3877–88 [Google Scholar]
  132. Nishimura K, Fukagawa T, Takisawa H, Kakimoto T, Kanemaki M. 132.  2009. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6:917–22 [Google Scholar]
  133. Odat O, Gardiner J, Sawchuk MG, Verna C, Donner TJ, Scarpella E. 133.  2014. Characterization of an allelic series in the MONOPTEROS gene of Arabidopsis. Genesis 52:127–33 [Google Scholar]
  134. Oh E, Zhu JY, Bai MY, Arenhart RA, Sun Y, Wang ZY. 134.  2014. Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. eLife 3:e03031 [Google Scholar]
  135. Oh E, Zhu JY, Ryu H, Hwang I, Wang ZY. 135.  2014. TOPLESS mediates brassinosteroid-induced transcriptional repression through interaction with BZR1. Nat. Commun. 5:4140 [Google Scholar]
  136. Ohashi-Ito K, Bergmann DC. 136.  2007. Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY. Development 134:2959–68 [Google Scholar]
  137. Ohashi-Ito K, Saegusa M, Iwamoto K, Oda Y, Katayama H. 137.  et al. 2014. A bHLH complex activates vascular cell division via cytokinin action in root apical meristem. Curr. Biol. 24:2053–58 [Google Scholar]
  138. Okada K, Ueda J, Komaki MK, Bell CJ, Shimura Y. 138.  1991. Requirement of the auxin polar transport system in early stages of Arabidopsis floral bud formation. Plant Cell 3:677–84 [Google Scholar]
  139. Ouellet F, Overvoorde PJ, Theologis A. 139.  2001. IAA17/AXR3: biochemical insight into an auxin mutant phenotype. Plant Cell 13:829–41 [Google Scholar]
  140. Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C. 140.  et al. 2005. Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell 17:3282–300 [Google Scholar]
  141. Paciorek T, Zazimalova E, Ruthardt N, Petrasek J, Stierhof YD. 141.  et al. 2005. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature 435:1251–56 [Google Scholar]
  142. Padmanabhan MS, Kramer SR, Wang X, Culver JN. 142.  2008. Tobacco mosaic virus replicase-auxin/indole acetic acid protein interactions: reprogramming the auxin response pathway to enhance virus infection. J. Virol. 82:2477–85 [Google Scholar]
  143. Parry G, Calderon-Villalobos LI, Prigge M, Peret B, Dharmasiri S. 143.  et al. 2009. Complex regulation of the TIR1/AFB family of auxin receptors. PNAS 106:22540–45 [Google Scholar]
  144. Peer WA. 144.  2013. From perception to attenuation: auxin signalling and responses. Curr. Opin. Plant Biol. 16:561–68 [Google Scholar]
  145. Pinon V, Prasad K, Grigg SP, Sanchez-Perez GF, Scheres B. 145.  2013. Local auxin biosynthesis regulation by PLETHORA transcription factors controls phyllotaxis in Arabidopsis. PNAS 110:1107–12 [Google Scholar]
  146. Piya S, Shrestha SK, Binder B, Stewart CN Jr, Hewezi T. 146.  2014. Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. Front. Plant Sci. 5:744 [Google Scholar]
  147. Plavskin Y, Timmermans MC. 147.  2012. Small RNA-regulated networks and the evolution of novel structures in plants. Cold Spring Harb. Symp. Quant. Biol. 77:221–33 [Google Scholar]
  148. Porcher A, Dostatni N. 148.  2010. The bicoid morphogen system. Curr. Biol. 20:R249–54 [Google Scholar]
  149. Prasad K, Grigg SP, Barkoulas M, Yadav RK, Sanchez-Perez GF. 149.  et al. 2011. Arabidopsis PLETHORA transcription factors control phyllotaxis. Curr. Biol. 21:1123–28 [Google Scholar]
  150. Prigge MJ, Lavy M, Ashton NW, Estelle M. 150.  2010. Physcomitrella patens auxin-resistant mutants affect conserved elements of an auxin-signaling pathway. Curr. Biol. 20:1907–12 [Google Scholar]
  151. Przemeck GK, Mattsson J, Hardtke CS, Sung ZR, Berleth T. 151.  1996. Studies on the role of the Arabidopsis gene MONOPTEROS in vascular development and plant cell axialization. Planta 200:229–37 [Google Scholar]
  152. Rademacher EH, Lokerse AS, Schlereth A, Llavata-Peris CI, Bayer M. 152.  et al. 2012. Different auxin response machineries control distinct cell fates in the early plant embryo. Dev. Cell 22:211–22 [Google Scholar]
  153. Rademacher EH, Möller B, Lokerse AS, Llavata-Peris CI, van den Berg W, Weijers D. 153.  2011. A cellular expression map of the Arabidopsis AUXIN RESPONSE FACTOR gene family. Plant J. 68:597–606 [Google Scholar]
  154. Ramos JA, Zenser N, Leyser O, Callis J. 154.  2001. Rapid degradation of auxin/indoleacetic acid proteins requires conserved amino acids of domain II and is proteasome dependent. Plant Cell 13:2349–60 [Google Scholar]
  155. Rashotte AM, Mason MG, Hutchison CE, Ferreira FJ, Schaller GE, Kieber JJ. 155.  2006. A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway. PNAS 103:11081–85 [Google Scholar]
  156. Reed JW. 156.  2001. Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci. 6:420–25 [Google Scholar]
  157. Reinhardt D, Mandel T, Kuhlemeier C. 157.  2000. Auxin regulates the initiation and radial position of plant lateral organs. Plant Cell 12:507–18 [Google Scholar]
  158. Reinhardt D, Pesce ER, Stieger P, Mandel T, Baltensperger K. 158.  et al. 2003. Regulation of phyllotaxis by polar auxin transport. Nature 426:255–60 [Google Scholar]
  159. Remington DL, Vision TJ, Guilfoyle TJ, Reed JW. 159.  2004. Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol. 135:1738–52 [Google Scholar]
  160. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A. 160.  et al. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319:64–69 [Google Scholar]
  161. Restrepo S, Zartman JJ, Basler K. 161.  2014. Coordination of patterning and growth by the morphogen DPP. Curr. Biol. 24:R245–55 [Google Scholar]
  162. Richter R, Behringer C, Zourelidou M, Schwechheimer C. 162.  2013. Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana. PNAS 110:13192–97 [Google Scholar]
  163. Robert HS, Crhak Khaitova L, Mroue S, Benkova E. 163.  2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. J. Exp. Bot. 66:5029–42 [Google Scholar]
  164. Robert HS, Grunewald W, Sauer M, Cannoot B, Soriano M. 164.  et al. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development 142:702–11 [Google Scholar]
  165. Robert S, Kleine-Vehn J, Barbez E, Sauer M, Paciorek T. 165.  et al. 2010. ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis. Cell 143:111–21 [Google Scholar]
  166. Rogg LE, Lasswell J, Bartel B. 166.  2001. A gain-of-function mutation in IAA28 suppresses lateral root development. Plant Cell 13:465–80 [Google Scholar]
  167. Ryu H, Cho H, Bae W, Hwang I. 167.  2014. Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3. Nat. Commun. 5:4138 [Google Scholar]
  168. Sabatini S, Beis D, Wolkenfelt H, Murfett J, Guilfoyle T. 168.  et al. 1999. An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell 99:463–72 [Google Scholar]
  169. Sachs T. 169.  2000. Integrating cellular and organismic aspects of vascular differentiation. Plant Cell Physiol. 41:649–56 [Google Scholar]
  170. Saiga S, Furumizu C, Yokoyama R, Kurata T, Sato S. 170.  et al. 2008. The Arabidopsis OBERON1 and OBERON2 genes encode plant homeodomain finger proteins and are required for apical meristem maintenance. Development 135:1751–59 [Google Scholar]
  171. Saiga S, Möller B, Watanabe-Taneda A, Abe M, Weijers D, Komeda Y. 171.  2012. Control of embryonic meristem initiation in Arabidopsis by PHD-finger protein complexes. Development 139:1391–98 [Google Scholar]
  172. Salehin M, Bagchi R, Estelle M. 172.  2015. SCFTIR1/AFB-based auxin perception: mechanism and role in plant growth and development. Plant Cell 27:9–19 [Google Scholar]
  173. Sato Y, Nishimura A, Ito M, Ashikari M, Hirano HY, Matsuoka M. 173.  2001. Auxin response factor family in rice. Genes Genet. Syst. 76:373–80 [Google Scholar]
  174. Sawa S, Watanabe K, Goto K, Liu YG, Shibata D. 174.  et al. 1999. FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes Dev. 13:1079–88 [Google Scholar]
  175. Scarpella E, Marcos D, Friml J, Berleth T. 175.  2006. Control of leaf vascular patterning by polar auxin transport. Genes Dev. 20:1015–27 [Google Scholar]
  176. Schenck D, Christian M, Jones A, Luthen H. 176.  2010. Rapid auxin-induced cell expansion and gene expression: a four-decade-old question revisited. Plant Physiol. 152:1183–85 [Google Scholar]
  177. Schlereth A, Möller B, Liu W, Kientz M, Flipse J. 177.  et al. 2010. MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Nature 464:913–16 [Google Scholar]
  178. Schuetz M, Berleth T, Mattsson J. 178.  2008. Multiple MONOPTEROS-dependent pathways are involved in leaf initiation. Plant Physiol. 148:870–80 [Google Scholar]
  179. Schuster C, Gaillochet C, Lohmann JU. 179.  2015. Arabidopsis HECATE genes function in phytohormone control during gynoecium development. Development 142:3343–50 [Google Scholar]
  180. Sessions RA, Nemhauser JL, McColl A, Roe JL, Feldmann KA, Zambryski PC. 180.  1997. ETTIN patterns the Arabidopsis floral meristem and reproductive organs. Development 124:4481–91 [Google Scholar]
  181. Sessions RA, Zambryski PC. 181.  1995. Arabidopsis gynoecium structure in the wild and in ettin mutants. Development 121:1519–32 [Google Scholar]
  182. Shin R, Burch AY, Huppert KA, Tiwari SB, Murphy AS. 182.  et al. 2007. The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell 19:2440–53 [Google Scholar]
  183. Siegfried KR, Eshed Y, Baum SF, Otsuga D, Drews GN, Bowman JL. 183.  1999. Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development 126:4117–28 [Google Scholar]
  184. Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P. 184.  et al. 2011. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147:1270–82 [Google Scholar]
  185. Smith RS, Guyomarc'h S, Mandel T, Reinhardt D, Kuhlemeier C, Prusinkiewicz P. 185.  2006. A plausible model of phyllotaxis. PNAS 103:1301–6 [Google Scholar]
  186. Steffens B, Feckler C, Palme K, Christian M, Bottger M, Luthen H. 186.  2001. The auxin signal for protoplast swelling is perceived by extracellular ABP1. Plant J. 27:591–99 [Google Scholar]
  187. Stepanova AN, Robertson-Hoyt J, Yun J, Benavente LM, Xie DY. 187.  et al. 2008. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell 133:177–91 [Google Scholar]
  188. Stuttmann J, Lechner E, Guerois R, Parker JE, Nussaume L. 188.  et al. 2009. COP9 signalosome- and 26S proteasome-dependent regulation of SCFTIR1 accumulation in Arabidopsis. J. Biol. Chem. 284:7920–30 [Google Scholar]
  189. Sugano SS, Shirakawa M, Takagi J, Matsuda Y, Shimada T. 189.  et al. 2014. CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol. 55:475–81 [Google Scholar]
  190. Sun B, Xu Y, Ng KH, Ito T. 190.  2009. A timing mechanism for stem cell maintenance and differentiation in the Arabidopsis floral meristem. Genes Dev. 23:1791–804 [Google Scholar]
  191. Suzuki M, Yamazaki C, Mitsui M, Kakei Y, Mitani Y. 191.  et al. 2015. Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis. Plant Cell Rep. 34:1343–52 [Google Scholar]
  192. Szemenyei H, Hannon M, Long JA. 192.  2008. TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science 319:1384–86 [Google Scholar]
  193. Tan X, Calderon-Villalobos LI, Sharon M, Zheng C, Robinson CV. 193.  et al. 2007. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446:640–45 [Google Scholar]
  194. Terrile MC, Paris R, Calderon-Villalobos LI, Iglesias MJ, Lamattina L. 194.  et al. 2012. Nitric oxide influences auxin signaling through S-nitrosylation of the Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 auxin receptor. Plant J. 70:492–500 [Google Scholar]
  195. Tiwari SB, Hagen G, Guilfoyle T. 195.  2003. The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533–43 [Google Scholar]
  196. Tiwari SB, Hagen G, Guilfoyle TJ. 196.  2004. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell 16:533–43 [Google Scholar]
  197. Tiwari SB, Wang XJ, Hagen G, Guilfoyle TJ. 197.  2001. AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin. Plant Cell 13:2809–22 [Google Scholar]
  198. To JP, Haberer G, Ferreira FJ, Deruere J, Mason MG. 198.  et al. 2004. Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. Plant Cell 16:658–71 [Google Scholar]
  199. Ulmasov T, Hagen G, Guilfoyle TJ. 199.  1997. ARF1, a transcription factor that binds to auxin response elements. Science 276:1865–68 [Google Scholar]
  200. Ulmasov T, Hagen G, Guilfoyle TJ. 200.  1999. Activation and repression of transcription by auxin-response factors. PNAS 96:5844–49 [Google Scholar]
  201. Ulmasov T, Hagen G, Guilfoyle TJ. 201.  1999. Dimerization and DNA binding of auxin response factors. Plant J. 19:309–19 [Google Scholar]
  202. Ulmasov T, Liu ZB, Hagen G, Guilfoyle TJ. 202.  1995. Composite structure of auxin response elements. Plant Cell 7:1611–23 [Google Scholar]
  203. Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ. 203.  1997. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9:1963–71 [Google Scholar]
  204. Vanneste S, Friml J. 204.  2009. Auxin: a trigger for change in plant development. Cell 136:1005–16 [Google Scholar]
  205. Varaud E, Brioudes F, Szecsi J, Leroux J, Brown S. 205.  et al. 2011. AUXIN RESPONSE FACTOR8 regulates Arabidopsis petal growth by interacting with the bHLH transcription factor BIGPETALp. Plant Cell 23:973–83 [Google Scholar]
  206. Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H. 206.  et al. 2011. The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol. Syst. Biol. 7:508 [Google Scholar]
  207. Vidal EA, Araus V, Lu C, Parry G, Green PJ. 207.  et al. 2010. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. PNAS 107:4477–82 [Google Scholar]
  208. Vieten A, Vanneste S, Wisniewska J, Benkova E, Benjamins R. 208.  et al. 2005. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development 132:4521–31 [Google Scholar]
  209. Wang JJ, Guo HS. 209.  2015. Cleavage of INDOLE-3-ACETIC ACID INDUCIBLE28 mRNA by microRNA847 upregulates auxin signaling to modulate cell proliferation and lateral organ growth in Arabidopsis. Plant Cell 27:574–90 [Google Scholar]
  210. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY. 210.  2005. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204–16 [Google Scholar]
  211. Wang S, Hagen G, Guilfoyle TJ. 211.  2013. ARF-Aux/IAA interactions through domain III/IV are not strictly required for auxin-responsive gene expression. Plant Signal. Behav. 8:e24526 [Google Scholar]
  212. Watson AD, Edmondson DG, Bone JR, Mukai Y, Yu Y. 212.  et al. 2000. Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev. 14:2737–44 [Google Scholar]
  213. Weigel D, Jurgens G. 213.  2002. Stem cells that make stems. Nature 415:751–54 [Google Scholar]
  214. Weijers D, Benkova E, Jager KE, Schlereth A, Hamann T. 214.  et al. 2005. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO J. 24:1874–85 [Google Scholar]
  215. Weijers D, Schlereth A, Ehrismann JS, Schwank G, Kientz M, Jurgens G. 215.  2006. Auxin triggers transient local signaling for cell specification in Arabidopsis embryogenesis. Dev. Cell 10:265–70 [Google Scholar]
  216. Weiste C, Droge-Laser W. 216.  2014. The Arabidopsis transcription factor bZIP11 activates auxin-mediated transcription by recruiting the histone acetylation machinery. Nat. Commun. 5:3883 [Google Scholar]
  217. Wenzel CL, Schuetz M, Yu Q, Mattsson J. 217.  2007. Dynamics of MONOPTEROS and PIN-FORMED1 expression during leaf vein pattern formation in Arabidopsis thaliana. Plant J. 49:387–98 [Google Scholar]
  218. Werner T, Motyka V, Laucou V, Smets R, Van Onckelen H, Schmülling T. 218.  2003. Cytokinin-deficient transgenic Arabidopsis plants show multiple developmental alterations indicating opposite functions of cytokinins in the regulation of shoot and root meristem activity. Plant Cell 15:2532–50 [Google Scholar]
  219. Windels D, Bielewicz D, Ebneter M, Jarmolowski A, Szweykowska-Kulinska Z, Vazquez F. 219.  2014. miR393 is required for production of proper auxin signalling outputs. PLOS ONE 9:e95972 [Google Scholar]
  220. Wolters H, Anders N, Geldner N, Gavidia R, Jurgens G. 220.  2011. Coordination of apical and basal embryo development revealed by tissue-specific GNOM functions. Development 138:117–26 [Google Scholar]
  221. Woo EJ, Marshall J, Bauly J, Chen JG, Venis M. 221.  et al. 2002. Crystal structure of auxin-binding protein 1 in complex with auxin. EMBO J. 21:2877–85 [Google Scholar]
  222. Worley CK, Zenser N, Ramos J, Rouse D, Leyser O. 222.  et al. 2000. Degradation of Aux/IAA proteins is essential for normal auxin signalling. Plant J. 21:553–62 [Google Scholar]
  223. Wu MF, Tian Q, Reed JW. 223.  2006. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133:4211–18 [Google Scholar]
  224. Wu MF, Yamaguchi N, Xiao J, Bargmann B, Estelle M. 224.  et al. 2015. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. eLife 4:e09269 [Google Scholar]
  225. Xu T, Dai N, Chen J, Nagawa S, Cao M. 225.  et al. 2014. Cell surface ABP1-TMK auxin-sensing complex activates ROP GTPase signaling. Science 343:1025–28 [Google Scholar]
  226. Xu T, Wen M, Nagawa S, Fu Y, Chen JG. 226.  et al. 2010. Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. Cell 143:99–110 [Google Scholar]
  227. Yamaguchi N, Jeong CW, Nole-Wilson S, Krizek B, Wagner D. 227.  2016. AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 induce LEAFY expression in response to auxin to promote the onset of flower formation in Arabidopsis. Plant Physiol. 170:283–93 [Google Scholar]
  228. Yamaguchi N, Wu MF, Winter CM, Berns MC, Nole-Wilson S. 228.  et al. 2013. A molecular framework for auxin-mediated initiation of flower primordia. Dev. Cell 24:271–82 [Google Scholar]
  229. Yang J, Tian L, Sun MX, Huang XY, Zhu J. 229.  et al. 2013. AUXIN RESPONSE FACTOR17 is essential for pollen wall pattern formation in Arabidopsis. Plant Physiol. 162:720–31 [Google Scholar]
  230. Yoon EK, Yang JH, Lim J, Kim SH, Kim SK, Lee WS. 230.  2010. Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res. 38:1382–91 [Google Scholar]
  231. Yoshida S, Barbier de Reuille P, Lane B, Bassel GW, Prusinkiewicz P. 231.  et al. 2014. Genetic control of plant development by overriding a geometric division rule. Dev. Cell 29:75–87 [Google Scholar]
  232. Yoshida S, Mandel T, Kuhlemeier C. 232.  2011. Stem cell activation by light guides plant organogenesis. Genes Dev. 25:1439–50 [Google Scholar]
  233. Yu H, Zhang Y, Moss BL, Bargmann BO, Wang R. 233.  et al. 2015. Untethering the TIR1 auxin receptor from the SCF complex increases its stability and inhibits auxin response. Nat. Plants 1:14030 [Google Scholar]
  234. Zenser N, Ellsmore A, Leasure C, Callis J. 234.  2001. Auxin modulates the degradation rate of Aux/IAA proteins. PNAS 98:11795–800 [Google Scholar]
  235. Zhang JY, He SB, Li L, Yang HQ. 235.  2014. Auxin inhibits stomatal development through MONOPTEROS repression of a mobile peptide gene STOMAGEN in mesophyll. PNAS 111:E3015–23 [Google Scholar]
  236. Zhao Y, Xing L, Wang X, Hou YJ, Gao J. 236.  et al. 2014. The ABA receptor PYL8 promotes lateral root growth by enhancing MYB77-dependent transcription of auxin-responsive genes. Sci. Signal. 7:ra53 [Google Scholar]
  237. Zhao Z, Andersen SU, Ljung K, Dolezal K, Miotk A. 237.  et al. 2010. Hormonal control of the shoot stem-cell niche. Nature 465:1089–92 [Google Scholar]
/content/journals/10.1146/annurev-arplant-043015-112122
Loading
Transcriptional Responses to the Auxin Hormone
Annual Review of Plant Biology 67, 539 (2016); https://doi.org/10.1146/annurev-arplant-043015-112122
/content/journals/10.1146/annurev-arplant-043015-112122
/content/journals/10.1146/annurev-arplant-043015-112122
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error