Transcriptional Responses to the Auxin Hormone.

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.

[1]  Alan M. Jones,et al.  ABP1 Mediates Auxin Inhibition of Clathrin-Dependent Endocytosis in Arabidopsis , 2010, Cell.

[2]  J. Bowman,et al.  A Simple Auxin Transcriptional Response System Regulates Multiple Morphogenetic Processes in the Liverwort Marchantia polymorpha , 2015, PLoS genetics.

[3]  Xuemei Chen,et al.  AGAMOUS Terminates Floral Stem Cell Maintenance in Arabidopsis by Directly Repressing WUSCHEL through Recruitment of Polycomb Group Proteins[W] , 2011, Plant Cell.

[4]  G. Jürgens,et al.  Coordination of apical and basal embryo development revealed by tissue-specific GNOM functions , 2011, Development.

[5]  J. Chory,et al.  Regulation of Auxin Response by the Protein Kinase PINOID , 2000, Cell.

[6]  G. Ditta,et al.  The HECATE genes regulate female reproductive tract development in Arabidopsis thaliana , 2007, Development.

[7]  G. Hagen,et al.  AUX/IAA Proteins Are Active Repressors, and Their Stability and Activity Are Modulated by Auxin Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010289. , 2001, The Plant Cell Online.

[8]  Alan M. Jones,et al.  Rapid Auxin-Induced Cell Expansion and Gene Expression: A Four-Decade-Old Question Revisited1[C][W] , 2010, Plant Physiology.

[9]  Konrad Basler,et al.  Coordination of Patterning and Growth by the Morphogen DPP , 2014, Current Biology.

[10]  J. Franco-Zorrilla,et al.  DNA-binding specificities of plant transcription factors and their potential to define target genes , 2014, Proceedings of the National Academy of Sciences.

[11]  D. Inzé,et al.  Auxin Transport Promotes Arabidopsis Lateral Root Initiation , 2001, Plant Cell.

[12]  Max H Nanao,et al.  Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression , 2014, Proceedings of the National Academy of Sciences.

[13]  K. Ng,et al.  A timing mechanism for stem cell maintenance and differentiation in the Arabidopsis floral meristem. , 2009, Genes & development.

[14]  Teva Vernoux,et al.  Structural basis for oligomerization of auxin transcriptional regulators , 2014, Nature Communications.

[15]  Travis W. Banks,et al.  Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana. , 1999, Genes & development.

[16]  E. Meyerowitz,et al.  TOPLESS Regulates Apical Embryonic Fate in Arabidopsis , 2006, Science.

[17]  C. Bell,et al.  Requirement of the Auxin Polar Transport System in Early Stages of Arabidopsis Floral Bud Formation. , 1991, The Plant cell.

[18]  M. Yanofsky,et al.  HALF FILLED promotes reproductive tract development and fertilization efficiency in Arabidopsis thaliana , 2011, Development.

[19]  M. Terrile,et al.  MiR393 Regulation of Auxin Signaling and Redox-Related Components during Acclimation to Salinity in Arabidopsis , 2014, PloS one.

[20]  D. Wagner,et al.  AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis1[OPEN] , 2015, Plant Physiology.

[21]  D. Shibata,et al.  FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. , 1999, Genes & development.

[22]  Christophe Godin,et al.  Cytokinin signalling inhibitory fields provide robustness to phyllotaxis , 2013, Nature.

[23]  G. Hagen,et al.  Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4 , 2004, Development.

[24]  Klaus Harter,et al.  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 , 2012, BMC Plant Biology.

[25]  S. Takada,et al.  Involvement of CUP-SHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana. , 2000, Plant & cell physiology.

[26]  Michael Sauer,et al.  Efflux-dependent auxin gradients establish the apical–basal axis of Arabidopsis , 2003, Nature.

[27]  C. Scutt,et al.  Evolution of the ARF gene family in land plants: old domains, new tricks. , 2013, Molecular biology and evolution.

[28]  R. Guérois,et al.  COP9 Signalosome- and 26S Proteasome-dependent Regulation of SCFTIR1 Accumulation in Arabidopsis* , 2009, Journal of Biological Chemistry.

[29]  Thorsten Hamann,et al.  Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators , 2005, The EMBO journal.

[30]  Soo-Hwan Kim,et al.  Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development , 2009, Nucleic acids research.

[31]  J. Ecker,et al.  Type-A Arabidopsis Response Regulators Are Partially Redundant Negative Regulators of Cytokinin Signaling Online version contains Web-only data. , 2004, The Plant Cell Online.

[32]  Iain W. Manfield,et al.  Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors , 2014, Cell.

[33]  R. Mann,et al.  Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins , 2011, Cell.

[34]  P. Becker,et al.  Histone acetylation: a switch between repressive and permissive chromatin , 2002, EMBO reports.

[35]  A. Jarmołowski,et al.  miR393 Is Required for Production of Proper Auxin Signalling Outputs , 2014, PloS one.

[36]  Teva Vernoux,et al.  Reporters for sensitive and quantitative measurement of auxin response , 2015, Nature Methods.

[37]  Michael H. Wilson,et al.  Unraveling the Evolution of Auxin Signaling1[C][W] , 2010, Plant Physiology.

[38]  Tom Beeckman,et al.  Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression , 2005, Development.

[39]  P. He,et al.  The Pseudomonas syringae Type III Effector AvrRpt2 Promotes Pathogen Virulence via Stimulating Arabidopsis Auxin/Indole Acetic Acid Protein Turnover1[C][W][OA] , 2013, Plant Physiology.

[40]  Christophe Godin,et al.  The auxin signalling network translates dynamic input into robust patterning at the shoot apex , 2011, Molecular systems biology.

[41]  J. Grosclaude,et al.  A Novel Immunological Approach Establishes That the Auxin-binding Protein, Nt-abp1, Is an Element Involved in Auxin Signaling at the Plasma Membrane* , 1999, The Journal of Biological Chemistry.

[42]  Zhenbiao Yang,et al.  Genome Sequencing of Arabidopsis abp1-5 Reveals Second-Site Mutations That May Affect Phenotypes , 2015, Plant Cell.

[43]  Pierre Barbier de Reuille,et al.  A bHLH complex controls embryonic vascular tissue establishment and indeterminate growth in Arabidopsis. , 2013, Developmental cell.

[44]  D. Stillman,et al.  Ssn6-Tup1 interacts with class I histone deacetylases required for repression. , 2000, Genes & development.

[45]  G. Hagen,et al.  Activation and repression of transcription by auxin-response factors. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[46]  J. Nemhauser,et al.  Untethering the TIR1 auxin receptor from the SCF complex increases its stability and inhibits auxin response , 2015, Nature Plants.

[47]  Alan M. Jones,et al.  Auxin Action in a Cell-Free System , 2003, Current Biology.

[48]  G. Jürgens,et al.  Auxin triggers transient local signaling for cell specification in Arabidopsis embryogenesis. , 2006, Developmental cell.

[49]  B. Causier,et al.  The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis1[W][OA] , 2011, Plant Physiology.

[50]  Thomas H. Clarke,et al.  Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato , 2014, Journal of experimental botany.

[51]  J. Bowman,et al.  Distinct Mechanisms Promote Polarity Establishment in Carpels of Arabidopsis , 1999, Cell.

[52]  Masashi Suzuki,et al.  Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis , 2015, Plant Cell Reports.

[53]  Joseph R. Ecker,et al.  Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation , 2005, Development.

[54]  G. Gheysen,et al.  Tightly controlled WRKY23 expression mediates Arabidopsis embryo development , 2013, EMBO reports.

[55]  W. Dröge-Laser,et al.  The Arabidopsis transcription factor bZIP11 activates auxin-mediated transcription by recruiting the histone acetylation machinery , 2014, Nature Communications.

[56]  R. Franks,et al.  Auxin and the Arabidopsis thaliana gynoecium. , 2013, Journal of experimental botany.

[57]  M. Estelle,et al.  Lysine Residues Are Not Required for Proteasome-Mediated Proteolysis of the Auxin/Indole Acidic Acid Protein IAA11[OPEN] , 2015, Plant Physiology.

[58]  J. Nemhauser,et al.  Untethering the TIR1 auxin receptor from the SCF complex increases its stability and inhibits auxin response. , 2015, Nature plants.

[59]  J. Reed,et al.  Roles and activities of Aux/IAA proteins in Arabidopsis. , 2001, Trends in plant science.

[60]  Klaus Palme,et al.  A PINOID-Dependent Binary Switch in Apical-Basal PIN Polar Targeting Directs Auxin Efflux , 2004, Science.

[61]  James Briscoe,et al.  Morphogen interpretation: the transcriptional logic of neural tube patterning. , 2013, Current opinion in genetics & development.

[62]  J. Friml,et al.  Control of leaf vascular patterning by polar auxin transport. , 2006, Genes & development.

[63]  Nathalie Dostatni,et al.  The Bicoid Morphogen System , 2010, Current Biology.

[64]  T. Vision,et al.  Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families1[w] , 2004, Plant Physiology.

[65]  G. Jürgens,et al.  The auxin-insensitive bodenlos mutation affects primary root formation and apical-basal patterning in the Arabidopsis embryo. , 1999, Development.

[66]  Dominique C Bergmann,et al.  Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY , 2007, Development.

[67]  B. Bartel,et al.  A Gain-of-Function Mutation in IAA28 Suppresses Lateral Root Development , 2001, Plant Cell.

[68]  S. Tabata,et al.  The Arabidopsis OBERON1 and OBERON2 genes encode plant homeodomain finger proteins and are required for apical meristem maintenance , 2008, Development.

[69]  J. Culver,et al.  Tobacco Mosaic Virus Replicase-Auxin/Indole Acetic Acid Protein Interactions: Reprogramming the Auxin Response Pathway To Enhance Virus Infection , 2007, Journal of Virology.

[70]  D. Wagner,et al.  A molecular framework for auxin-mediated initiation of flower primordia. , 2013, Developmental cell.

[71]  C. Schwechheimer,et al.  Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana , 2013, Proceedings of the National Academy of Sciences.

[72]  J L Bowman,et al.  Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. , 1999, Development.

[73]  J. Alvarez,et al.  Morphogenesis in pinoid mutants of Arabidopsis thaliana , 1995 .

[74]  M. Lenhard,et al.  SLOW MOTION Is Required for Within-Plant Auxin Homeostasis and Normal Timing of Lateral Organ Initiation at the Shoot Meristem in Arabidopsis[C][W] , 2010, Plant Cell.

[75]  G. Coruzzi,et al.  Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana , 2010, Proceedings of the National Academy of Sciences.

[76]  Jonathan D. G. Jones,et al.  A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling , 2006, Science.

[77]  J. Nemhauser,et al.  ETTIN patterns the Arabidopsis floral meristem and reproductive organs. , 1997, Development.

[78]  S. Masiero,et al.  An integrative model of the control of ovule primordia formation. , 2013, The Plant journal : for cell and molecular biology.

[79]  Ottoline Leyser,et al.  Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins , 2001, Nature.

[80]  J. Kieber,et al.  A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[81]  Bruno Müller,et al.  Cytokinin and auxin interaction in root stem-cell specification during early embryogenesis , 2008, Nature.

[82]  D. Weijers,et al.  Auxin control of embryo patterning. , 2009, Cold Spring Harbor perspectives in biology.

[83]  M. Bennett,et al.  Plant embryogenesis requires AUX/LAX-mediated auxin influx , 2015, Development.

[84]  J. Reed,et al.  Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction , 2006, Development.

[85]  Pierre Barbier de Reuille,et al.  Computer simulations reveal novel properties of the cell-cell signaling network at the shoot apex in /Arabidopsis , 2005 .

[86]  D. Cleveland,et al.  Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells , 2012, Proceedings of the National Academy of Sciences.

[87]  M. Crespi,et al.  miR390, Arabidopsis TAS3 tasiRNAs, and Their AUXIN RESPONSE FACTOR Targets Define an Autoregulatory Network Quantitatively Regulating Lateral Root Growth[W] , 2010, Plant Cell.

[88]  Qi Xie,et al.  Pattern of Auxin and Cytokinin Responses for Shoot Meristem Induction Results from the Regulation of Cytokinin Biosynthesis by AUXIN RESPONSE FACTOR31[W][OA] , 2012, Plant Physiology.

[89]  E. Meyerowitz,et al.  Patterns of Auxin Transport and Gene Expression during Primordium Development Revealed by Live Imaging of the Arabidopsis Inflorescence Meristem , 2005, Current Biology.

[90]  C. Kuhlemeier,et al.  Stem cell activation by light guides plant organogenesis. , 2011, Genes & development.

[91]  Anna N. Stepanova,et al.  TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development , 2008, Cell.

[92]  Masashi Yamada,et al.  Plant development is regulated by a family of auxin receptor F box proteins. , 2005, Developmental cell.

[93]  Adam M. Gustafson,et al.  microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants , 2005, Cell.

[94]  M. Estelle,et al.  Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development , 2015, Proceedings of the National Academy of Sciences.

[95]  J. Nemhauser,et al.  Rate Motifs Tune Auxin/Indole-3-Acetic Acid Degradation Dynamics1[OPEN] , 2015, Plant Physiology.

[96]  D. Weijers,et al.  The PINOID protein kinase regulates organ development in Arabidopsis by enhancing polar auxin transport. , 2001, Development.

[97]  Charles W. Melnyk,et al.  A Developmental Framework for Graft Formation and Vascular Reconnection in Arabidopsis thaliana , 2015, Current Biology.

[98]  D. Inzé,et al.  Bimodular auxin response controls organogenesis in Arabidopsis , 2010, Proceedings of the National Academy of Sciences.

[99]  G. Hagen,et al.  ARF1, a transcription factor that binds to auxin response elements. , 1997, Science.

[100]  J. Ecker,et al.  Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana[W] , 2005, The Plant Cell Online.

[101]  Xu Chen,et al.  Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules , 2014, Nature.

[102]  A. Theologis,et al.  IAA17/AXR3: Biochemical Insight into an Auxin Mutant Phenotype , 2001, Plant Cell.

[103]  E. Mjolsness,et al.  An auxin-driven polarized transport model for phyllotaxis , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[104]  P. Perez,et al.  AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. , 1996, The Plant cell.

[105]  H. Lilie,et al.  Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response , 2013, Proceedings of the National Academy of Sciences.

[106]  J. Long,et al.  TOPLESS Mediates Auxin-Dependent Transcriptional Repression During Arabidopsis Embryogenesis , 2008, Science.

[107]  J. Long,et al.  APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19 , 2012, Development.

[108]  J. Callis,et al.  Auxin modulates the degradation rate of Aux/IAA proteins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[109]  D. Ware,et al.  Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays , 2012, PloS one.

[110]  J. Bennetzen,et al.  The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , 2008, Science.

[111]  T. Berleth,et al.  Multiple MONOPTEROS-Dependent Pathways Are Involved in Leaf Initiation1[C][W][OA] , 2008, Plant Physiology.

[112]  Lei Gao,et al.  DNA Topoisomerase I Affects Polycomb Group Protein-Mediated Epigenetic Regulation and Plant Development by Altering Nucleosome Distribution in Arabidopsis[W] , 2014, The Plant Cell.

[113]  G. Hagen,et al.  ARF-Aux/IAA interactions through domain III/IV are not strictly required for auxin-responsive gene expression , 2013, Plant signaling & behavior.

[114]  J. Nemhauser,et al.  Auxin and ETTIN in Arabidopsis gynoecium morphogenesis. , 2000, Development.

[115]  P. He,et al.  Pseudomonas syringae type III effector AvrRpt2 alters Arabidopsis thaliana auxin physiology , 2007, Proceedings of the National Academy of Sciences.

[116]  Yunde Zhao,et al.  Auxin Synthesized by the YUCCA Flavin Monooxygenases Is Essential for Embryogenesis and Leaf Formation in Arabidopsis[W] , 2007, The Plant Cell Online.

[117]  F. Sánchez,et al.  MicroRNAs as regulators in plant metal toxicity response , 2012, Front. Plant Sci..

[118]  G. Jürgens,et al.  The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS-mediated embryo patterning. , 2002, Genes & development.

[119]  S. Abel,et al.  Aux/IAA proteins are phosphorylated by phytochrome in vitro. , 2000, Plant physiology.

[120]  J. Bowman,et al.  Efficient and Inducible Use of Artificial MicroRNAs in Marchantia polymorpha. , 2016, Plant & cell physiology.

[121]  Valérie Laucou,et al.  Cytokinin-Deficient Transgenic Arabidopsis Plants Show Multiple Developmental Alterations Indicating Opposite Functions of Cytokinins in the Regulation of Shoot and Root Meristem Activity Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.014928 , 2003, The Plant Cell Online.

[122]  Jennifer Moon,et al.  A New CULLIN 1 Mutant Has Altered Responses to Hormones and Light in Arabidopsis1[C][OA] , 2006, Plant Physiology.

[123]  A. Theologis,et al.  Degradation of Aux/IAA proteins is essential for normal auxin signalling. , 2000, The Plant journal : for cell and molecular biology.

[124]  S. Tiwari,et al.  Aux/IAA Proteins Contain a Potent Transcriptional Repression Domain , 2004, The Plant Cell Online.

[125]  Stig U. Andersen,et al.  Hormonal control of the shoot stem-cell niche , 2010, Nature.

[126]  M. Heisler,et al.  SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein. , 2001, Development.

[127]  D. Patel,et al.  Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF , 2006, Nature.

[128]  B. Cairns,et al.  The biology of chromatin remodeling complexes. , 2009, Annual review of biochemistry.

[129]  V. Mironova,et al.  Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome , 2014, BMC Genomics.

[130]  Eric Klavins,et al.  A Synthetic Approach Reveals Extensive Tunability of Auxin Signaling1[C][W][OA] , 2012, Plant Physiology.

[131]  Ying Fu,et al.  Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis , 2010, Cell.

[132]  Gabino Sanchez-Perez,et al.  Local auxin biosynthesis regulation by PLETHORA transcription factors controls phyllotaxis in Arabidopsis , 2012, Proceedings of the National Academy of Sciences.

[133]  Eunkyoo Oh,et al.  Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl , 2014, eLife.

[134]  A. Theologis,et al.  ThePS-IAA4/5-like Family of Early Auxin-inducible mRNAs inArabidopsis thaliana , 1995 .

[135]  G. Krouk,et al.  A map of cell type-specific auxin responses , 2013, Molecular systems biology.

[136]  K. Dreher,et al.  The Arabidopsis Aux/IAA Protein Family Has Diversified in Degradation and Auxin Responsiveness[W] , 2006, The Plant Cell Online.

[137]  Tatsuo Fukagawa,et al.  An auxin-based degron system for the rapid depletion of proteins in nonplant cells , 2009, Nature Methods.

[138]  Hong-Wei Xue,et al.  Control of Root Cap Formation by MicroRNA-Targeted Auxin Response Factors in Arabidopsisw⃞ , 2005, The Plant Cell Online.

[139]  T. Schmülling,et al.  Cytokinin Regulates the Activity of Reproductive Meristems, Flower Organ Size, Ovule Formation, and Thus Seed Yield in Arabidopsis thaliana[C][W][OA] , 2011, Plant Cell.

[140]  Xiaohong Zhu,et al.  The ABA Receptor PYL8 Promotes Lateral Root Growth by Enhancing MYB77-Dependent Transcription of Auxin-Responsive Genes , 2014, Science Signaling.

[141]  P. Benfey,et al.  Organization and cell differentiation in lateral roots of Arabidopsis thaliana. , 1997, Development.

[142]  Zhongchi Liu,et al.  A model for an early role of auxin in Arabidopsis gynoecium morphogenesis , 2014, Front. Plant Sci..

[143]  R. Mann,et al.  Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness , 2015, Cell.

[144]  Karine David,et al.  Conditional Repression of AUXIN BINDING PROTEIN1 Reveals That It Coordinates Cell Division and Cell Expansion during Postembryonic Shoot Development in Arabidopsis and Tobacco[W] , 2008, The Plant Cell Online.

[145]  D. Weigel,et al.  Integration of floral inductive signals in Arabidopsis , 2000, Nature.

[146]  J. Memelink,et al.  Auxin-induced, SCF(TIR1)-mediated poly-ubiquitination marks AUX/IAA proteins for degradation. , 2009, The Plant Journal.

[147]  C. Kuhlemeier,et al.  Auxin Regulates the Initiation and Radial Position of Plant Lateral Organs , 2000, Plant Cell.

[148]  T. Girin,et al.  INDEHISCENT and SPATULA Interact to Specify Carpel and Valve Margin Tissue and Thus Promote Seed Dispersal in Arabidopsis[W] , 2011, Plant Cell.

[149]  Jan Willem Borst,et al.  Different auxin response machineries control distinct cell fates in the early plant embryo. , 2012, Developmental cell.

[150]  M. Timmermans,et al.  Small RNA-regulated networks and the evolution of novel structures in plants. , 2012, Cold Spring Harbor symposia on quantitative biology.

[151]  Hongquan Yang,et al.  Auxin inhibits stomatal development through MONOPTEROS repression of a mobile peptide gene STOMAGEN in mesophyll , 2014, Proceedings of the National Academy of Sciences.

[152]  C. N. Stewart,et al.  Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis , 2014, Front. Plant Sci..

[153]  Gerhard K. H. Przemeck,et al.  Studies on the role of the Arabidopsis gene MONOPTEROS in vascular development and plant cell axialization , 2004, Planta.

[154]  C. Perrot-Rechenmann,et al.  AUXIN RESPONSE FACTOR8 Regulates Arabidopsis Petal Growth by Interacting with the bHLH Transcription Factor BIGPETALp[C][W] , 2011, Plant Cell.

[155]  P. Prusinkiewicz,et al.  A plausible model of phyllotaxis , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[156]  N. Grimsley,et al.  Analysis of gametophytic development in the moss, Physcomitrella patens, using auxin and cytokinin resistant mutants , 2004, Planta.

[157]  T. Guilfoyle The PB1 Domain in Auxin Response Factor and Aux/IAA Proteins: A Versatile Protein Interaction Module in the Auxin Response[OPEN] , 2015, Plant Cell.

[158]  Alan M. Jones,et al.  Cell Surface ABP1-TMK Auxin-Sensing Complex Activates ROP GTPase Signaling , 2014, Science.

[159]  Daniel P. Schachtman,et al.  The Arabidopsis Transcription Factor MYB77 Modulates Auxin Signal Transduction[W] , 2007, The Plant Cell Online.

[160]  M. Barton,et al.  Twenty years on: the inner workings of the shoot apical meristem, a developmental dynamo. , 2010, Developmental biology.

[161]  C. Tsang,et al.  Nutrient regulates Tor1 nuclear localization and association with rDNA promoter , 2006, Nature.

[162]  O. Leyser,et al.  Rapid Degradation of Auxin/Indoleacetic Acid Proteins Requires Conserved Amino Acids of Domain II and Is Proteasome Dependent , 2001, The Plant Cell Online.

[163]  T. Sachs Integrating cellular and organismic aspects of vascular differentiation. , 2000, Plant & cell physiology.

[164]  D. Wagner,et al.  Integration of growth and patterning during vascular tissue formation in Arabidopsis , 2014, Science.

[165]  Jiayang Li,et al.  Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors , 2015, Science Advances.

[166]  G. Jürgens,et al.  The role of the monopteros gene in organising the basal body region of the Arabidopsis embryo , 1993 .

[167]  G. Hagen,et al.  Composite structure of auxin response elements. , 1995, The Plant cell.

[168]  M. Matsuoka,et al.  Auxin response factor family in rice. , 2001, Genes & genetic systems.

[169]  M. Sussman,et al.  ABP1 is required for organized cell elongation and division in Arabidopsis embryogenesis. , 2001, Genes & development.

[170]  M. Schmid,et al.  MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor , 2010, Nature.

[171]  T. Sun,et al.  Isolation and Characterization of cul1-7, a Recessive Allele of CULLIN1 That Disrupts SCF Function at the C Terminus of CUL1 in Arabidopsis thaliana , 2009, Genetics.

[172]  H. Fukuda,et al.  A bHLH Complex Activates Vascular Cell Division via Cytokinin Action in Root Apical Meristem , 2014, Current Biology.

[173]  John L. Bowman,et al.  Green Genes—Comparative Genomics of the Green Branch of Life , 2007, Cell.

[174]  M. Estelle,et al.  Report Physcomitrella Patens Auxin-resistant Mutants Affect Conserved Elements of an Auxin-signaling Pathway , 2022 .

[175]  Transcriptional repression caused by Dof5.8 is involved in proper vein network formation in Arabidopsis thaliana leaves , 2015, Journal of Plant Research.

[176]  Yunde Zhao,et al.  Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. , 2006, Genes & development.

[177]  Hui Guo,et al.  Cleavage of INDOLE-3-ACETIC ACID INDUCIBLE28 mRNA by MicroRNA847 Upregulates Auxin Signaling to Modulate Cell Proliferation and Lateral Organ Growth in Arabidopsis , 2015, Plant Cell.

[178]  J. Long,et al.  Genetic control of distal stem cell fate within root and embryonic meristems , 2015, Science.

[179]  Xue-Yong Huang,et al.  AUXIN RESPONSE FACTOR17 Is Essential for Pollen Wall Pattern Formation in Arabidopsis1[C][W][OA] , 2013, Plant Physiology.

[180]  C. Hardtke,et al.  The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development , 1998, The EMBO journal.

[181]  E. Meyerowitz,et al.  LEAFY controls auxin response pathways in floral primordium formation. , 2013, Science signaling.

[182]  G. Hagen,et al.  Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. , 1997, The Plant cell.

[183]  G. Hagen,et al.  Soybean GH3 promoter contains multiple auxin-inducible elements. , 1994, The Plant cell.

[184]  M. Estelle,et al.  Arabidopsis AXR6 encodes CUL1 implicating SCF E3 ligases in auxin regulation of embryogenesis , 2003, The EMBO journal.

[185]  S. Xiao,et al.  Cell differentiation and germ–soma separation in Ediacaran animal embryo-like fossils , 2014, Nature.

[186]  J. Fernández,et al.  A functional interaction between the histone deacetylase Rpd3 and the corepressor groucho in Drosophila development. , 1999, Genes & development.

[187]  M. Estelle,et al.  The axr6 mutants of Arabidopsis thaliana define a gene involved in auxin response and early development. , 2000, Development.

[188]  Jun Xiao,et al.  Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate , 2015, eLife.

[189]  Laila Moubayidin,et al.  Dynamic Control of Auxin Distribution Imposes a Bilateral-to-Radial Symmetry Switch during Gynoecium Development , 2015, Current Biology.

[190]  Mukesh Jain,et al.  Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa) , 2005, Functional & Integrative Genomics.

[191]  H. Ryu,et al.  Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3 , 2014, Nature Communications.

[192]  Jens Keilwagen,et al.  De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference , 2011, PLoS Comput. Biol..

[193]  E. Herman,et al.  KDEL-Containing Auxin-Binding Protein Is Secreted to the Plasma Membrane and Cell Wall , 1993, Plant physiology.

[194]  P. Oeller,et al.  Early auxin-induced genes encode short-lived nuclear proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[195]  P. Prusinkiewicz,et al.  Genetic control of plant development by overriding a geometric division rule. , 2014, Developmental cell.

[196]  John Chandler,et al.  DORNRÖSCHEN is a direct target of the auxin response factor MONOPTEROS in the Arabidopsis embryo , 2009, Development.

[197]  Jason Gardiner,et al.  Characterization of an allelic series in the MONOPTEROS gene of arabidopsis , 2014, Genesis.

[198]  M. Estelle,et al.  SCFTIR1/AFB-Based Auxin Perception: Mechanism and Role in Plant Growth and Development , 2015, Plant Cell.

[199]  K. Palme,et al.  The auxin signal for protoplast swelling is perceived by extracellular ABP1. , 2001, The Plant journal : for cell and molecular biology.

[200]  Xuemei Chen,et al.  AUXIN RESPONSE FACTOR 3 integrates the functions of AGAMOUS and APETALA2 in floral meristem determinacy. , 2014, The Plant journal : for cell and molecular biology.

[201]  C. D. de Oliveira,et al.  A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin , 2012, Nature chemical biology.

[202]  M. Bennett,et al.  Regulation of phyllotaxis by polar auxin transport , 2003, Nature.

[203]  Ottoline Leyser,et al.  An Auxin-Dependent Distal Organizer of Pattern and Polarity in the Arabidopsis Root , 1999, Cell.

[204]  M. Estelle,et al.  AXL and AXR1 have redundant functions in RUB conjugation and growth and development in Arabidopsis. , 2007, The Plant journal : for cell and molecular biology.

[205]  T. Kohchi,et al.  CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. , 2014, Plant & cell physiology.

[206]  Michael S. Barker,et al.  The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants , 2011, Science.

[207]  Enrico Scarpella,et al.  Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves , 2009, Development.

[208]  Qiang Yu,et al.  Dynamics of MONOPTEROS and PIN-FORMED1 expression during leaf vein pattern formation in Arabidopsis thaliana. , 2007, The Plant journal : for cell and molecular biology.

[209]  Steffen Vanneste,et al.  Auxin: A Trigger for Change in Plant Development , 2009, Cell.

[210]  D. Hwang,et al.  A secreted peptide acts on BIN2-mediated phosphorylation of ARFs to potentiate auxin response during lateral root development , 2013, Nature Cell Biology.

[211]  B. Snel,et al.  Arabidopsis PLETHORA Transcription Factors Control Phyllotaxis , 2011, Current Biology.

[212]  Michal Sharon,et al.  Mechanism of auxin perception by the TIR1 ubiquitin ligase , 2007, Nature.

[213]  Tom Beeckman,et al.  A novel sensor to map auxin response and distribution at high spatio-temporal resolution , 2012, Nature.

[214]  M. Goldsmith,et al.  Rapid response of the plasma-membrane potential in oat coleoptiles to auxin and other weak acids , 1983, Planta.

[215]  J. Lohmann,et al.  Arabidopsis HECATE genes function in phytohormone control during gynoecium development , 2015, Development.

[216]  G. Neuhaus,et al.  Auxin-induced developmental patterns in Brassica juncea embryos. , 1998, Development.

[217]  D. Weijers,et al.  A cellular expression map of the Arabidopsis AUXIN RESPONSE FACTOR gene family. , 2011, The Plant journal : for cell and molecular biology.

[218]  Eunkyoo Oh,et al.  TOPLESS mediates brassinosteroid-induced transcriptional repression through interaction with BZR1 , 2014, Nature Communications.

[219]  R. Pickersgill,et al.  Crystal structure of auxin‐binding protein 1 in complex with auxin , 2002, The EMBO journal.

[220]  M. Terrile,et al.  Nitric oxide influences auxin signaling through S-nitrosylation of the Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 auxin receptor. , 2012, The Plant journal : for cell and molecular biology.

[221]  Gerald A Tuskan,et al.  Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa , 2007, BMC Plant Biology.

[222]  M. Estelle,et al.  Role of the Arabidopsis RING-H2 Protein RBX1 in RUB Modification and SCF Function Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003178. , 2002, The Plant Cell Online.

[223]  E. Benková,et al.  The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. , 2015, Journal of experimental botany.

[224]  W. Peer From perception to attenuation: auxin signalling and responses. , 2013, Current opinion in plant biology.

[225]  H. Fukaki,et al.  Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 gene of Arabidopsis. , 2002, The Plant journal : for cell and molecular biology.

[226]  Mineko Konishi,et al.  MONOPTEROS directly activates the auxin-inducible promoter of the Dof5.8 transcription factor gene in Arabidopsis thaliana leaf provascular cells , 2014, Journal of experimental botany.

[227]  David A. Morris,et al.  Auxin inhibits endocytosis and promotes its own efflux from cells , 2005, Nature.

[228]  M. Estelle,et al.  The F-box protein TIR1 is an auxin receptor , 2005, Nature.

[229]  N. Chua,et al.  Auxin Polar Transport Is Essential for the Establishment of Bilateral Symmetry during Early Plant Embryogenesis. , 1993, The Plant cell.

[230]  G. Hagen,et al.  Dimerization and DNA binding of auxin response factors. , 1999, The Plant journal : for cell and molecular biology.

[231]  P. Zambryski,et al.  Arabidopsis gynoecium structure in the wild and in ettin mutants. , 1995, Development.

[232]  G. Hagen,et al.  The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.008417. , 2003, The Plant Cell Online.

[233]  Detlef Weigel,et al.  Stem cells that make stems , 2002, Nature.

[234]  Christian S. Hardtke,et al.  Hormone Signalling Crosstalk in Plant Growth Regulation , 2011, Current Biology.

[235]  M. Estelle,et al.  Complex regulation of the TIR1/AFB family of auxin receptors , 2009, Proceedings of the National Academy of Sciences.

[236]  D. Weijers,et al.  Control of embryonic meristem initiation in Arabidopsis by PHD-finger protein complexes , 2012, Development.