AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip

Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO3−) and phosphate (PO43−) are also signaling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signaling pathways are integrated. Here we report the identification of a highly NO3−-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory-elements. We demonstrate that this transcription factor and a close homolog repress primary root growth in response to P deficiency conditions, but only when NO3− is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO3− and P signaling converge via double transcriptional and post-transcriptional control of the same protein, HRS1

[1]  Javier Paz-Ares,et al.  A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis , 2010, PLoS genetics.

[2]  V. Rubio,et al.  A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. , 2001, Genes & development.

[3]  Peng Wang,et al.  GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis[W][OA] , 2009, The Plant Cell Online.

[4]  P. Benfey,et al.  Transcriptional Regulation of ROS Controls Transition from Proliferation to Differentiation in the Root , 2010, Cell.

[5]  Gabriel Krouk,et al.  Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis , 2010, BMC Systems Biology.

[6]  Rodrigo A Gutiérrez,et al.  A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. , 2008, Current opinion in plant biology.

[7]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[8]  Gabriel Krouk,et al.  Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis , 2014, Proceedings of the National Academy of Sciences.

[9]  A. Millar,et al.  TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock in Arabidopsis thaliana[W][OA] , 2010, Plant Cell.

[10]  S. Rothstein,et al.  Genetic Regulation by NLA and MicroRNA827 for Maintaining Nitrate-Dependent Phosphate Homeostasis in Arabidopsis , 2011, PLoS genetics.

[11]  R. Gutiérrez,et al.  Integration of local and systemic signaling pathways for plant N responses. , 2012, Current opinion in plant biology.

[12]  Laurent Nussaume,et al.  Root tip contact with low-phosphate media reprograms plant root architecture , 2007, Nature Genetics.

[13]  Felipe F. Aceituno,et al.  Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. , 2014, The Plant journal : for cell and molecular biology.

[14]  C. Ticconi,et al.  ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability , 2009, Proceedings of the National Academy of Sciences.

[15]  Fabian Kellermeier,et al.  Analysis of the Root System Architecture of Arabidopsis Provides a Quantitative Readout of Crosstalk between Nutritional Signals[W][OPEN] , 2014, Plant Cell.

[16]  R. Gutiérrez,et al.  Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[17]  Yann LeCun,et al.  Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate , 2010, Genome Biology.

[18]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[19]  Mineko Konishi,et al.  Arabidopsis NIN-like transcription factors have a central role in nitrate signalling , 2013, Nature Communications.

[20]  F. Maestre,et al.  Decoupling of soil nutrient cycles as a function of aridity in global drylands , 2013, Nature.

[21]  T. Chiou,et al.  NITROGEN LIMITATION ADAPTATION, a Target of MicroRNA827, Mediates Degradation of Plasma Membrane–Localized Phosphate Transporters to Maintain Phosphate Homeostasis in Arabidopsis[W][OPEN] , 2013, Plant Cell.

[22]  J. J. Camacho-Cristóbal,et al.  PRD, an ArabidopsisAINTEGUMENTA-like gene, is involved in root architectural changes in response to phosphate starvation , 2008, Planta.

[23]  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.

[24]  Rodrigo A. Gutiérrez,et al.  Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments , 2014, Front. Plant Sci..

[25]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[26]  T. Fujiwara,et al.  A nitrate-inducible GARP family gene encodes an auto-repressible transcriptional repressor in rice. , 2013, Plant & cell physiology.

[27]  P. L. Rodriguez,et al.  HRS1 Acts as a Negative Regulator of Abscisic Acid Signaling to Promote Timely Germination of Arabidopsis Seeds , 2012, PloS one.

[28]  S. Rothstein,et al.  Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene , 2008, Journal of experimental botany.

[29]  Jennifer L. Nemhauser,et al.  Different Plant Hormones Regulate Similar Processes through Largely Nonoverlapping Transcriptional Responses , 2006, Cell.

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

[31]  Swetlana Friedel,et al.  Plasticity of the Arabidopsis Root System under Nutrient Deficiencies1[C][W][OPEN] , 2013, Plant Physiology.

[32]  N. Chua,et al.  NITROGEN LIMITATION ADAPTATION Recruits PHOSPHATE2 to Target the Phosphate Transporter PT2 for Degradation during the Regulation of Arabidopsis Phosphate Homeostasis[W] , 2014, Plant Cell.

[33]  C. Maurel,et al.  A proteomic study reveals novel insights into the diversity of aquaporin forms expressed in the plasma membrane of plant roots. , 2003, The Biochemical journal.

[34]  Rodrigo A. Gutiérrez,et al.  VirtualPlant: A Software Platform to Support Systems Biology Research1[W][OA] , 2009, Plant Physiology.

[35]  Gabriel Krouk,et al.  Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants. , 2010, Developmental cell.

[36]  Dennis Shasha,et al.  A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis , 2009, PLoS Comput. Biol..

[37]  Gabriel Krouk,et al.  A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule" , 2009, BMC Systems Biology.

[38]  Y. Tsay,et al.  CHL1 Functions as a Nitrate Sensor in Plants , 2009, Cell.

[39]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[40]  K. Shinozaki,et al.  Generation of chimeric repressors that confer salt tolerance in Arabidopsis and rice. , 2011, Plant biotechnology journal.

[41]  Zhou Du,et al.  agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..

[42]  Gloria Coruzzi,et al.  Genomic Analysis of the Nitrate Response Using a Nitrate Reductase-Null Mutant of Arabidopsis1[w] , 2004, Plant Physiology.

[43]  L. Nussaume,et al.  Root developmental adaptation to phosphate starvation: better safe than sorry. , 2011, Trends in plant science.

[44]  B. Lahner,et al.  Arabidopsis pdr2 reveals a phosphate-sensitive checkpoint in root development. , 2004, The Plant journal : for cell and molecular biology.

[45]  B. Forde,et al.  Nitrate signalling mediated by the NRT1.1 nitrate transporter antagonises L-glutamate-induced changes in root architecture. , 2008, The Plant journal : for cell and molecular biology.

[46]  R. Kerstetter,et al.  KANADI regulates organ polarity in Arabidopsis , 2001, Nature.

[47]  T. Lamaze,et al.  Adaptation of the Photosynthetic Apparatus in Maize Leaves as a Result of Nitrogen Limitation : Relationships between Electron Transport and Carbon Assimilation. , 1990, Plant physiology.

[48]  G. Krouk,et al.  Nitrate signaling: adaptation to fluctuating environments. , 2010, Current opinion in plant biology.

[49]  V. Colot,et al.  Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants , 2013, Nature Communications.

[50]  U. Grossniklaus,et al.  A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta[w] , 2003, Plant Physiology.

[51]  Y. Tsay,et al.  AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. , 2009, The Plant journal : for cell and molecular biology.

[52]  K. Mayer,et al.  GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana. , 2013, The Plant journal : for cell and molecular biology.

[53]  Daowen Wang,et al.  Overexpressing HRS1 confers hypersensitivity to low phosphate-elicited inhibition of primary root growth in Arabidopsis thaliana. , 2009, Journal of integrative plant biology.

[54]  Gabriel Krouk,et al.  TARGET: a transient transformation system for genome-wide transcription factor target discovery. , 2013, Molecular plant.

[55]  Rongchen Wang,et al.  A Genetic Screen for Nitrate Regulatory Mutants Captures the Nitrate Transporter Gene NRT1.11[W][OA] , 2009, Plant Physiology.

[56]  Mark Stitt,et al.  Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w] , 2004, Plant Physiology.

[57]  B. Mueller‐Roeber,et al.  Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development , 2014, Nature Communications.

[58]  K. Miura,et al.  The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[59]  A. Gojon,et al.  Root uptake regulation: a central process for NPS homeostasis in plants. , 2009, Current opinion in plant biology.