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Plant Biology

  • Open Access
    Widespread inter‐individual gene expression variability in Arabidopsis thaliana
    Widespread inter‐individual gene expression variability in <em>Arabidopsis thaliana</em>
    1. Sandra Cortijo1,
    2. Zeynep Aydin1,
    3. Sebastian Ahnert1 and
    4. James CW Locke (james.locke{at}slcu.cam.ac.uk)*,1
    1. 1The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
    1. ↵*Corresponding author. Tel: +44 1223 761110; E‐mail: james.locke{at}slcu.cam.ac.uk

    RNA‐seq on individual seedlings is used to detect inter‐individual gene expression variability in Arabidopsis thaliana. 9% of the transcriptome is identified as highly variable for at least one time point during the day/night cycle.

    Synopsis

    RNA‐seq on individual seedlings is used to detect inter‐individual gene expression variability in Arabidopsis thaliana. 9% of the transcriptome is identified as highly variable for at least one time point during the day/night cycle.

    • Two sets of highly variable genes were identified, either mainly variable during the day or night.

    • Highly variable genes tend to be involved in the response to the environment.

    • Highly variable genes tend to be shorter, to be targeted by a higher number of transcription factors and to be characterised by a “closed” chromatin environment.

    • Gene expression variability for individual genes of interest can be viewed on https://jlgroup.shinyapps.io/AraNoisy/.

    • Arabidopsis thaliana
    • inter‐individual heterogeneity
    • noise in gene expression
    • RNA‐seq
    • transcriptional variability

    Mol Syst Biol. (2019) 15: e8591

    • Received August 9, 2018.
    • Revision received December 7, 2018.
    • Accepted December 11, 2018.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Sandra Cortijo, Zeynep Aydin, Sebastian Ahnert, James CW Locke
    Published online 24.01.2019
  • Open Access
    Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
    Photoperiodic control of the <em>Arabidopsis</em> proteome reveals a translational coincidence mechanism
    1. Daniel D Seaton1,4,†,
    2. Alexander Graf2,5,†,
    3. Katja Baerenfaller2,6,
    4. Mark Stitt3,
    5. Andrew J Millar (andrew.millar{at}ed.ac.uk)*,1 and
    6. Wilhelm Gruissem (wgruisse{at}ethz.ch)*,2
    1. 1SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
    2. 2Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
    3. 3System Regulation Group, Max Planck Institute of Molecular Plant Physiology, Potsdam‐Golm, Germany
    4. 4Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
    5. 5Present Address: Plant Proteomics Group, Max Planck Institute of Molecular Plant Physiology, Potsdam‐Golm, Germany
    6. 6Present Address: Swiss Institute of Allergy and Asthma Research, University of Zürich, Davos, Switzerland
    1. ↵* Corresponding author. Tel: +44 131 651 3325; Email: andrew.millar{at}ed.ac.uk
      Corresponding author. Tel: +41 44 632 0857; Email: wgruisse{at}ethz.ch

    1. ↵† These authors contributed equally to this work

    The Arabidopsis proteome changes in a coordinated fashion across four photoperiods. A simple “translational coincidence” mechanism can explain photoperiod‐dependent regulation of protein levels based on clock‐dependent, daily mRNA level changes.

    Synopsis

    The Arabidopsis proteome changes in a coordinated fashion across four photoperiods. A simple ‘translational coincidence’ mechanism can explain photoperiod‐dependent regulation of protein levels based on clock‐dependent, daily mRNA level changes.

    • Day length altered the abundance of 1,781 proteins, out of 4,344 proteins quantified from leaves of Arabidopsis thaliana, in a pattern consistent with higher metabolic activity in long days.

    • Proteins with clock‐regulated, evening‐peaking RNAs tended to increase in abundance under longer daylengths, whereas proteins with morning‐peaking RNAs did not.

    • A simple, “translational coincidence” model predicted the experimental results, because high, light‐induced translation rates will coincide with high levels of an evening‐expressed RNA only under long days, not short days.

    • Many clock‐controlled genes might gain seasonal control of protein levels via translational coincidence, which we speculate is widespread based upon data from a marine alga and a freshwater cyanobacterium.

    • circadian rhythms
    • metabolism
    • photoperiod
    • proteomics
    • seasonality

    Mol Syst Biol. (2018) 14: e7962

    • Received August 29, 2017.
    • Revision received January 22, 2018.
    • Accepted January 30, 2018.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Daniel D Seaton, Alexander Graf, Katja Baerenfaller, Mark Stitt, Andrew J Millar, Wilhelm Gruissem
    Published online 01.03.2018
  • Open Access
    A Sizer model for cell differentiation in Arabidopsis thaliana root growth
    A Sizer model for cell differentiation in <em>Arabidopsis thaliana</em> root growth
    1. Irina Pavelescu1,2,
    2. Josep Vilarrasa‐Blasi1,4,
    3. Ainoa Planas‐Riverola1,
    4. Mary‐Paz González‐García1,5,
    5. Ana I Caño‐Delgado (ana.cano{at}cragenomica.es)*,1,† and
    6. Marta Ibañes (mibanes{at}ub.edu)*,2,3,†
    1. 1Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC‐IRTA‐UAB‐UB, Campus UAB Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
    2. 2Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
    3. 3Universitat de Barcelona Institute of Complex Systems (UBICS) Universitat de Barcelona, Barcelona, Spain
    4. 4Present Address: Carnegie Institution for Science Department of Plant Biology, Stanford, CA, USA
    5. 5Present Address: Centro Nacional de Biotecnología‐CSIC, Madrid, Spain
    1. ↵* Corresponding author. Tel: +34 93 563 66 00 Ext. 3210; Fax: +34 93 563 66 01; E‐mail: ana.cano{at}cragenomica.es
      Corresponding author. Tel: +34 93 403 91 77; E‐mail: mibanes{at}ub.edu

    1. ↵† These authors contributed equally to this work

    Mathematical modeling and quantitative data on phenotypic variability from wild‐type Arabidopsis roots indicate that cells measure their length to stop elongating in primary roots.

    Synopsis

    Mathematical modeling and quantitative data on phenotypic variability from wild‐type Arabidopsis roots indicate that cells measure their length to stop elongating in primary roots.

    • Cell length quantification in single roots along the meristem and the elongation zone allows exploring relationships between phenotypic traits.

    • Computational analyses evaluate the plausibility of three models to stop cell elongation in roots: whether cells measure distances, time, or cell size.

    • The primary root growth is consistent with a Sizer mechanism, in which cells stop elongating when reaching a threshold cell length.

    • Brassinosteroid signaling at the meristem is sufficient to set the mature cell length.

    • Arabidopsis root zonation
    • brassinosteroids
    • cell differentiation
    • computational analysis
    • phenotypic variability

    Mol Syst Biol. (2018) 14: e7687

    • Received April 12, 2017.
    • Revision received November 21, 2017.
    • Accepted November 27, 2017.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Irina Pavelescu, Josep Vilarrasa‐Blasi, Ainoa Planas‐Riverola, Mary‐Paz González‐García, Ana I Caño‐Delgado, Marta Ibañes
    Published online 10.01.2018
  • Open Access
    From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress
    From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress
    1. Lisa Van den Broeck1,2,†,
    2. Marieke Dubois1,2,4,†,
    3. Mattias Vermeersch1,2,
    4. Veronique Storme1,2,
    5. Minami Matsui3 and
    6. Dirk Inzé (dirk.inze{at}psb.vib-ugent.be)*,1,2
    1. 1Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
    2. 2VIB Center for Plant Systems Biology, Ghent, Belgium
    3. 3RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
    4. 4Present Address: Institut de Biologie Moléculaire des Plantes, CNRS, Strasbourg, France
    1. ↵*Corresponding author. Tel: +32 9 331 38 06; E‐mail: dirk.inze{at}psb.vib-ugent.be

    1. ↵† These authors contributed equally to this work

    This study unravels a transcriptional network controlling Arabidopsis leaf growth inhibition in response to osmotic stress. The network consists of 20 transcription factors, whose complex and redundant patterns of interconnections enable robust adaptation to environmental changes.

    Synopsis

    This study unravels a transcriptional network controlling Arabidopsis leaf growth inhibition in response to osmotic stress. The network consists of 20 transcription factors, whose complex and redundant patterns of interconnections enable robust adaptation to environmental changes.

    • Linear pathways are a simplification. Multiple transcription factors can regulate the same target genes and, in some cases more than one transcription factor is necessary to induce the expression of a target gene.

    • The network is robust because regulatory redundancy is built in, making the network less susceptible to mutations. ERF6 and ERF98 are both induced in the first induction group and can transcriptionally activate a large part of the network. They have an overlap of 6 target genes. ERF8 and ERF9 are both induced in the third induction group and can transcriptionally repress a large part of the network, showing an overlap of 9 target genes.

    • The network is efficient for environmental adaption to a stress signal. The repressing activities in the network after 2 h of stress enables the network to return to its prestimulus state.

    • The network is highly responsive to a range of input signals and might be part of a general stress response. However, the need for two transcription factors to transactivate target genes prevents stochastic activation of the network. The random induction of the network would lead to a needless stress response which is disadvantageous for the plant.

    • growth regulation
    • mild osmotic stress
    • short‐term stress response
    • transcription factors
    • transcriptional network

    Mol Syst Biol. (2017) 13: 961

    • Received June 23, 2017.
    • Revision received November 25, 2017.
    • Accepted November 29, 2017.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Lisa Van den Broeck, Marieke Dubois, Mattias Vermeersch, Veronique Storme, Minami Matsui, Dirk Inzé
    Published online 21.12.2017
  • Open Access
    Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis
    Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <em>Arabidopsis</em>
    1. Markus Hartl1,2,3,†,
    2. Magdalena Füßl1,2,4,†,
    3. Paul J Boersema5,9,
    4. Jan‐Oliver Jost6,10,
    5. Katharina Kramer1,
    6. Ahmet Bakirbas1,4,11,
    7. Julia Sindlinger6,
    8. Magdalena Plöchinger2,
    9. Dario Leister2,
    10. Glen Uhrig7,
    11. Greg BG Moorhead7,
    12. Jürgen Cox5,
    13. Michael E Salvucci8,
    14. Dirk Schwarzer6,
    15. Matthias Mann5 and
    16. Iris Finkemeier (iris.finkemeier{at}uni-muenster.de)*,1,2,4
    1. 1Plant Proteomics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
    2. 2Plant Molecular Biology, Department Biology I, Ludwig‐Maximilians‐University Munich, Martinsried, Germany
    3. 3Mass Spectrometry Facility, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
    4. 4Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
    5. 5Proteomics and Signal Transduction, Max‐Planck Institute of Biochemistry, Martinsried, Germany
    6. 6Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
    7. 7Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
    8. 8US Department of Agriculture, Agricultural Research Service, Arid‐Land Agricultural Research Center, Maricopa, AZ, USA
    9. 9Present Address: Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
    10. 10Present Address: Leibniz‐Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
    11. 11Present Address: Plant Biology Graduate Program University of Massachusetts Amherst, Amherst, USA
    1. ↵*Corresponding author. Tel: +49 251 8323805; E‐mail: iris.finkemeier{at}uni-muenster.de

    1. ↵† These authors contributed equally to this work

    A comprehensive lysine acetylome profiling identifies new potential substrate proteins of the Arabidopsis RPD3/HDA1‐KDACs with various subcellular localizations. HDA14 is identified as the first RPD3/HDA1‐KDAC, which is active in organelles.

    Synopsis

    A comprehensive lysine acetylome profiling identifies new potential substrate proteins of the Arabidopsis RPD3/HDA1‐KDACs with various subcellular localizations. HDA14 is identified as the first RPD3/HDA1‐KDAC, which is active in organelles.

    • 2,152 lysine acetylation sites are identified on 1,022 Arabidopsis protein groups.

    • Analyses with deacetylase inhibitors identify potential target sites of RPD3/HDA1 class‐KDACs of Arabidopsis.

    • HDA14 is found to be active in Arabidopsis chloroplasts and RuBisCo activase (RCA) Kac‐438 is identified as one of the potential HDA14 substrates.

    • Lysine acetylation on RCA‐K438 decreases the enzyme's ADP‐sensitivity, which is important for RCA inhibition under low‐light conditions.

    • Arabidopsis
    • histone deacetylases
    • lysine acetylation
    • photosynthesis
    • RuBisCO activase

    Mol Syst Biol. (2017) 13: 949

    • Received June 16, 2017.
    • Revision received September 22, 2017.
    • Accepted September 25, 2017.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Markus Hartl, Magdalena Füßl, Paul J Boersema, Jan‐Oliver Jost, Katharina Kramer, Ahmet Bakirbas, Julia Sindlinger, Magdalena Plöchinger, Dario Leister, Glen Uhrig, Greg BG Moorhead, Jürgen Cox, Michael E Salvucci, Dirk Schwarzer, Matthias Mann, Iris Finkemeier
    Published online 23.10.2017
  • Open Access
    Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
    Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
    1. Daniel D Seaton1,†,
    2. Robert W Smith14†,
    3. Young Hun Song25,
    4. Dana R MacGregor36,
    5. Kelly Stewart1,
    6. Gavin Steel1,
    7. Julia Foreman1,
    8. Steven Penfield36,
    9. Takato Imaizumi2,
    10. Andrew J Millar1 and
    11. Karen J Halliday*,1
    1. 1SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
    2. 2Department of Biology, University of Washington, Seattle, WA, USA
    3. 3Biosciences, University of Exeter, Exeter, UK
    4. 4Laboratory of Systems & Synthetic Biology, Wageningen UR, Wageningen, The Netherlands
    5. 5Department of Life Sciences, Ajou University, Suwon, South Korea
    6. 6Department of Crop Genetics, John Innes Centre, Norwich, UK
    1. ↵*Corresponding author. Tel: +44 131 651 9083; E‐mail: karen.halliday{at}ed.ac.uk

    Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling.

    Synopsis

    Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling.

    • CCA1 negatively regulates FKF1 and CDF1 transcription.

    • GI has an FKF1‐independent role in CDF1 protein stabilisation.

    • PIF proteins function throughout light:dark cycles.

    • Temperature regulates flowering time and hypocotyl elongation pathways at distinct times of day.

    • gene regulatory networks
    • heat
    • hypocotyl elongation
    • photoperiodism
    • seasonal breeding

    Mol Syst Biol. (2015) 11: 776

    • Received September 15, 2014.
    • Revision received November 21, 2014.
    • Accepted December 5, 2014.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Daniel D Seaton, Robert W Smith, Young Hun Song, Dana R MacGregor, Kelly Stewart, Gavin Steel, Julia Foreman, Steven Penfield, Takato Imaizumi, Andrew J Millar, Karen J Halliday
    Published online 19.01.2015
  • Open Access
    An organ boundary‐enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
    An organ boundary‐enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
    1. Caihuan Tian1,
    2. Xiaoni Zhang1,2,
    3. Jun He1,
    4. Haopeng Yu1,3,
    5. Ying Wang1,
    6. Bihai Shi1,3,
    7. Yingying Han1,3,
    8. Guoxun Wang1,3,
    9. Xiaoming Feng1,
    10. Cui Zhang1,
    11. Jin Wang1,3,
    12. Jiyan Qi1,3,
    13. Rong Yu2 and
    14. Yuling Jiao*,1
    1. 1State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China
    2. 2College of Life Sciences, Capital Normal University, Beijing, China
    3. 3University of Chinese Academy of Sciences, Beijing, China
    1. ↵*Corresponding author. Tel: +86 10 64807656; Fax: +86 10 64806595; E‐mail: yljiao{at}genetics.ac.cn

    The leaf boundary regions separate differentiated organs from undifferentiated stem cells in plants. The gene regulatory network of boundary cells was mapped by combining cell type‐specific genome expression analysis with genomewide yeast one‐hybrid screening.

    Synopsis

    The leaf boundary regions separate differentiated organs from undifferentiated stem cells in plants. The gene regulatory network of boundary cells was mapped by combining cell type‐specific genome expression analysis with genomewide yeast one‐hybrid screening.

    • A leaf boundary cell‐specific gene expression map identifies transcriptional signatures and predicts cellular functions.

    • A genomewide protein–DNA interaction map resolved using a yeast one‐hybrid approach uncovers promoter hubs and predicts new regulating transcription factors (TFs).

    • An intermediate‐scale experimental test determined the regulatory effects of many TFs on their targets and identified new regulators and regulatory relationships in boundary and axillary meristem formation.

    • axillary meristem
    • gene regulatory network
    • organ boundary

    Mol Syst Biol. (2014) 10: 755

    • Received June 3, 2014.
    • Revision received August 14, 2014.
    • Accepted September 24, 2014.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Caihuan Tian, Xiaoni Zhang, Jun He, Haopeng Yu, Ying Wang, Bihai Shi, Yingying Han, Guoxun Wang, Xiaoming Feng, Cui Zhang, Jin Wang, Jiyan Qi, Rong Yu, Yuling Jiao
    Published online 30.10.2014
  • Open Access
    Plasma membrane H+‐ATPase regulation is required for auxin gradient formation preceding phototropic growth
    Plasma membrane H<sup>+</sup>‐ATPase regulation is required for auxin gradient formation preceding phototropic growth
    1. Tim Hohm1,2,†,
    2. Emilie Demarsy3,†,
    3. Clément Quan3,
    4. Laure Allenbach Petrolati3,
    5. Tobias Preuten3,
    6. Teva Vernoux4,
    7. Sven Bergmann*,1,2,‡ and
    8. Christian Fankhauser*,3,‡
    1. 1Department of Medical Genetics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
    2. 2Swiss Institute for Bioinformatics, Lausanne, Switzerland
    3. 3Centre for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
    4. 4Laboratoire de Reproduction et Développement des Plantes, CNRS INRA ENS Lyon UCBL Université de Lyon, Lyon, France
    1. ↵* Corresponding author. Tel: +41 21 692 5452; E‐mail: sven.bergmann{at}unil.ch
      Corresponding author. Tel: +41 21 692 3941; E‐mail: christian.fankhauser{at}unil.ch

    1. ↵† These authors contributed equally to this work

    2. ↵‡ These authors contributed equally to this work

    In silico and in planta analyses of the contribution of morphological and biophysical parameters to auxin relocalization in phototropism reveal the importance of light‐dependent regulation of apoplastic pH and of cellular topology.

    Synopsis

    In silico and in planta analyses of the contribution of morphological and biophysical parameters to auxin relocalization in phototropism reveal the importance of light‐dependent regulation of apoplastic pH and of cellular topology.

    • Regulation of apoplastic pH is a key feature for the establishment of a lateral auxin gradient leading to phototropism.

    • The phototropin photoreceptors regulate the activity of plasma membrane‐associated H+‐ATPase which are major regulators of apoplastic pH.

    • Cellular topology has a strong impact on lateral auxin gradient formation.

    • auxin
    • modeling
    • phototropins
    • phototropism
    • plasma membrane H+‐ATPase

    Mol Syst Biol. (2014) 10: 751

    • Received March 2, 2014.
    • Revision received August 20, 2014.
    • Accepted August 22, 2014.

    This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Tim Hohm, Emilie Demarsy, Clément Quan, Laure Allenbach Petrolati, Tobias Preuten, Teva Vernoux, Sven Bergmann, Christian Fankhauser
    Published online 26.09.2014
  • Open Access
    Sequential induction of auxin efflux and influx carriers regulates lateral root emergence
    1. Benjamin Péret1,2,3,†,
    2. Alistair M Middleton1,2,4,†,‡,
    3. Andrew P French1,2,
    4. Antoine Larrieu1,2,
    5. Anthony Bishopp1,2,5,
    6. Maria Njo6,7,
    7. Darren M Wells1,2,
    8. Silvana Porco1,2,
    9. Nathan Mellor1,2,
    10. Leah R Band1,2,4,
    11. Ilda Casimiro8,
    12. Jürgen Kleine‐Vehn6,7,
    13. Steffen Vanneste6,7,
    14. Ilkka Sairanen9,
    15. Romain Mallet1,2,
    16. Göran Sandberg10,
    17. Karin Ljung9,
    18. Tom Beeckman6,7,
    19. Eva Benkova6,7,
    20. Jiří Friml6,7,
    21. Eric Kramer11,
    22. John R King1,4,
    23. Ive De Smet2,6,7,
    24. Tony Pridmore1,
    25. Markus Owen1,4 and
    26. Malcolm J Bennett*,1,2
    1. 1 Centre for Plant Integrative Biology, University of Nottingham, Loughborough, UK
    2. 2 Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, UK
    3. 3 Unité Mixte de Recherche 7265, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Aix‐Marseille Université, Laboratoire de Biologie du Développement des Plantes, Saint‐Paul‐lez‐Durance, France
    4. 4 Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
    5. 5 Department of Biosciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    6. 6 Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent, Belgium
    7. 7 Department of Plant Biotechnology and Genetics, Ghent University, Ghent, Belgium
    8. 8 Universidad de Extremadura, Facultad de Ciencias, Badajoz, Spain
    9. 9 Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
    10. 10 Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
    11. 11 Physics Department, Simon's Rock College, Great Barrington, MA, USA
    1. ↵*Corresponding author. Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, Leics LE12 5RD, UK. Tel.:+44 115 951 3255; Fax:+44 115 951 6334; E‐mail: malcolm.bennett{at}nottingham.ac.uk

    1. ↵† These authors contributed equally to this work.

    • ↵‡ Present address: University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.

    Emergence of a new lateral root primordium through the outer layers of the parental root requires the sequential auxin‐mediated induction of two auxin transporters. This positive feedback regulatory loop coordinates patterned gene expression in outer tissues.

    Synopsis

    Emergence of a new lateral root primordium through the outer layers of the parental root requires the sequential auxin‐mediated induction of two auxin transporters. This positive feedback regulatory loop coordinates patterned gene expression in outer tissues.

    • The emergence of lateral roots through several tissues requires the precise regulation of gene expression in overlaying cells to trigger cell separation.

    • Auxin derived from new lateral root primordia induces a positive feedback loop in the outer tissues by promoting the expression of the auxin influx transporter LAX3.

    • A mathematical model based on realistic 3D geometries predicted the involvement of an auxin efflux carrier that was later identified to be PIN3.

    • The model also revealed that PIN3 must be expressed before LAX3 to ensure a ‘robust’ pattern of LAX3 induction in just two overlaying cortical cell files, thereby delimiting cell separation.

    • 3D modelling
    • auxin transport
    • lateral root emergence
    • ODE

    Mol Syst Biol. 9: 699

    • Received March 15, 2013.
    • Accepted August 6, 2013.

    This is an open‐access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.

    Benjamin Péret, Alistair M Middleton, Andrew P French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren M Wells, Silvana Porco, Nathan Mellor, Leah R Band, Ilda Casimiro, Jürgen Kleine‐Vehn, Steffen Vanneste, Ilkka Sairanen, Romain Mallet, Göran Sandberg, Karin Ljung, Tom Beeckman, Eva Benkova, Jiří Friml, Eric Kramer, John R King, Ive De Smet, Tony Pridmore, Markus Owen, Malcolm J Bennett
    Published online 22.10.2013
  • Open Access
    A map of cell type‐specific auxin responses
    1. Bastiaan O R Bargmann1,2,
    2. Steffen Vanneste3,4,
    3. Gabriel Krouk5,
    4. Tal Nawy1,
    5. Idan Efroni1,
    6. Eilon Shani2,
    7. Goh Choe2,
    8. Jiří Friml3,4,6,
    9. Dominique C Bergmann7,
    10. Mark Estelle2 and
    11. Kenneth D Birnbaum*,1
    1. 1 Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
    2. 2 Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
    3. 3 Department of Plant Systems Biology, VIB, Ghent, Belgium
    4. 4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
    5. 5 Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes—Claude Grignon, Montpellier, France
    6. 6 Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
    7. 7 Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
    1. ↵*Corresponding author. Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA. Tel.:+1 212 998 8257; Fax:+1 212 995 4015; E‐mail: ken.birnbaum{at}nyu.edu

    The transcriptional response to auxin was analyzed in four root cell types. The newly obtained data were cross‐referenced with spatial expression maps to examine auxin's role in regulating gene expression in the root meristem.

    Synopsis

    The transcriptional response to auxin was analyzed in four root cell types. The newly obtained data were cross‐referenced with spatial expression maps to examine auxin's role in regulating gene expression in the root meristem.

    • The majority of the thousands of auxin‐responsive genes in the Arabidopsis thaliana root show a spatial bias in their induction or repression by auxin treatment.

    • Auxin promotes the expression of cell‐identity markers for the developing xylem and quiescent center, whereas it inhibits markers for the maturing xylem, cortex and trichoblasts.

    • Relative induction or repression by auxin predicts expression along the longitudinal axis of the root.

    • Arabidopsis
    • development
    • root apical meristem
    • signaling gradient

    Mol Syst Biol. 9: 688

    • Received March 13, 2013.
    • Accepted July 23, 2013.

    This is an open‐access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.

    Bastiaan O R Bargmann, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, Jiří Friml, Dominique C Bergmann, Mark Estelle, Kenneth D Birnbaum
    Published online 10.09.2013

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