A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem

The root meristem (RM) is a fundamental structure that is responsible for postembryonic root growth. The RM contains the quiescent center (QC), stem cells and frequently dividing meristematic cells, in which the timing and the frequency of cell division are tightly regulated. In Arabidopsis thaliana, several gain-of-function analyses have demonstrated that peptide ligands of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) family are important for maintaining RM size. Here, we demonstrate that a plant U-box E3 ubiquitin ligase, PUB4, is a novel downstream component of CLV3/CLE signaling in the RM. Mutations in PUB4 reduced the inhibitory effect of exogenous CLV3/CLE peptide on root cell proliferation and columella stem cell maintenance. Moreover, pub4 mutants grown without exogenous CLV3/CLE peptide exhibited characteristic phenotypes in the RM, such as enhanced root growth, increased number of cortex/endodermis stem cells and decreased number of columella layers. Our phenotypic and gene expression analyses indicated that PUB4 promotes expression of a cell cycle regulatory gene, CYCD6;1, and regulates formative periclinal asymmetric cell divisions in endodermis and cortex/endodermis initial daughters. These data suggest that PUB4 functions as a global regulator of cell proliferation and the timing of asymmetric cell division that are important for final root architecture. Highlighted article: The Arabidopsis E3 ubiquitin ligase PUB4 acts downstream of the CLV3/CLE peptides to regulate stem cell division and patterning in the growing root.

[1]  S. Sabatini,et al.  Plant and animal stem cells: similar yet different , 2014, Nature Reviews Molecular Cell Biology.

[2]  Tasuku Ito,et al.  Plant GSK3 proteins regulate xylem cell differentiation downstream of TDIF–TDR signalling , 2014, Nature Communications.

[3]  H. Berg,et al.  The Arabidopsis U-box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility. , 2013, The Plant journal : for cell and molecular biology.

[4]  K. Gallagher,et al.  Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning , 2013, Development.

[5]  C. Seidel,et al.  Moderation of Arabidopsis Root Stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 Receptor Kinase Complexes , 2013, Current Biology.

[6]  M. Yamada,et al.  The roles of peptide hormones during plant root development. , 2013, Current opinion in plant biology.

[7]  T. Fujiwara,et al.  Identification of an EMS-induced causal mutation in a gene required for boron-mediated root development by low-coverage genome re-sequencing in Arabidopsis , 2012, Plant signaling & behavior.

[8]  Xiaohong Wang,et al.  Synergistic interaction of CLAVATA1, CLAVATA2, and RECEPTOR-LIKE PROTEIN KINASE 2 in cyst nematode parasitism of Arabidopsis. , 2013, Molecular plant-microbe interactions : MPMI.

[9]  Ryan G. Anderson,et al.  The Ubiquitin Ligase PUB22 Targets a Subunit of the Exocyst Complex Required for PAMP-Triggered Responses in Arabidopsis [C][W] , 2012, Plant Cell.

[10]  James A.H. Murray,et al.  A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division , 2012, Cell.

[11]  Shuang Wu,et al.  The SHORT-ROOT protein acts as a mobile, dose-dependent signal in patterning the ground tissue , 2012, Proceedings of the National Academy of Sciences.

[12]  Elliot M. Meyerowitz,et al.  Cytokinin signaling as a positional cue for patterning the apical–basal axis of the growing Arabidopsis shoot meristem , 2012, Proceedings of the National Academy of Sciences.

[13]  M. Yamada,et al.  The Function of the CLE Peptides in Plant Development and Plant-Microbe Interactions , 2011, The arabidopsis book.

[14]  P. He,et al.  Direct Ubiquitination of Pattern Recognition Receptor FLS2 Attenuates Plant Innate Immunity , 2011, Science.

[15]  J. Kieber,et al.  CLE Peptides can Negatively Regulate Protoxylem Vessel Formation via Cytokinin Signaling , 2010, Plant & cell physiology.

[16]  Yuriko Osakabe,et al.  RPK2 is an essential receptor-like kinase that transmits the CLV3 signal in Arabidopsis , 2010, Development.

[17]  L. Deslandes,et al.  The Medicago truncatula E3 Ubiquitin Ligase PUB1 Interacts with the LYK3 Symbiotic Receptor and Negatively Regulates Infection and Nodulation[W][OA] , 2010, Plant Cell.

[18]  Karen S. Osmont,et al.  Comprehensive Analysis of CLE Polypeptide Signaling Gene Expression and Overexpression Activity in Arabidopsis1[C][W][OA] , 2010, Plant Physiology.

[19]  Y. Matsubayashi,et al.  Secreted Peptide Signals Required for Maintenance of Root Stem Cell Niche in Arabidopsis , 2010, Science.

[20]  P. Benfey,et al.  Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth , 2010, Nature.

[21]  J. Friml,et al.  Auxin regulates distal stem cell differentiation in Arabidopsis roots , 2010, Proceedings of the National Academy of Sciences.

[22]  Renze Heidstra,et al.  SCHIZORIZA Encodes a Nuclear Factor Regulating Asymmetry of Stem Cell Divisions in the Arabidopsis Root , 2010, Current Biology.

[23]  H. Fukuda,et al.  Regulation of vascular development by CLE peptide-receptor systems. , 2010, Journal of integrative plant biology.

[24]  V. Chickarmane,et al.  Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem , 2009, Proceedings of the National Academy of Sciences.

[25]  Y. Kamiya,et al.  Autophagy Negatively Regulates Cell Death by Controlling NPR1-Dependent Salicylic Acid Signaling during Senescence and the Innate Immune Response in Arabidopsis[W][OA] , 2009, The Plant Cell Online.

[26]  R. Simon,et al.  A Signaling Module Controlling the Stem Cell Niche in Arabidopsis Root Meristems , 2009, Current Biology.

[27]  D. Goring,et al.  The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates. , 2009, Journal of experimental botany.

[28]  Takashi Aoyama,et al.  A Genetic Framework for the Control of Cell Division and Differentiation in the Root Meristem , 2008, Science.

[29]  H. Fukuda,et al.  The Receptor-Like Kinase SOL2 Mediates CLE Signaling in Arabidopsis , 2008, Plant & cell physiology.

[30]  Y. Mudgil,et al.  Interactions between the S-Domain Receptor Kinases and AtPUB-ARM E3 Ubiquitin Ligases Suggest a Conserved Signaling Pathway in Arabidopsis1[W][OA] , 2008, Plant Physiology.

[31]  John Runions,et al.  High-Resolution Whole-Mount Imaging of Three-Dimensional Tissue Organization and Gene Expression Enables the Study of Phloem Development and Structure in Arabidopsis[W] , 2008, The Plant Cell Online.

[32]  Rüdiger Simon,et al.  The Receptor Kinase CORYNE of Arabidopsis Transmits the Stem Cell–Limiting Signal CLAVATA3 Independently of CLAVATA1[W] , 2008, The Plant Cell Online.

[33]  Xiaohong Wang,et al.  Diverse and conserved roles of CLE peptides. , 2008, Current opinion in plant biology.

[34]  Yasukazu Nakamura,et al.  Gain-of-function phenotypes of chemically synthetic CLAVATA3/ESR-related (CLE) peptides in Arabidopsis thaliana and Oryza sativa. , 2007, Plant & cell physiology.

[35]  Renze Heidstra,et al.  Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action. , 2007, Genes & development.

[36]  Teva Vernoux,et al.  An Evolutionarily Conserved Mechanism Delimiting SHR Movement Defines a Single Layer of Endodermis in Plants , 2007, Science.

[37]  Renze Heidstra,et al.  Cytokinins Determine Arabidopsis Root-Meristem Size by Controlling Cell Differentiation , 2007, Current Biology.

[38]  M. Lenhard,et al.  Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers , 2007, Nature.

[39]  R. Motohashi,et al.  The FOX hunting system: an alternative gain-of-function gene hunting technique. , 2006, The Plant journal : for cell and molecular biology.

[40]  Hiroo Fukuda,et al.  A Plant Peptide Encoded by CLV3 Identified by in Situ MALDI-TOF MS Analysis , 2006, Science.

[41]  C. Ampomah-Dwamena,et al.  Gain-of-Function Phenotypes of Many CLAVATA3/ESR Genes, Including Four New Family Members, Correlate with Tandem Variations in the Conserved CLAVATA3/ESR Domain1[W] , 2006, Plant Physiology.

[42]  Wolfgang Busch,et al.  WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators , 2005, Nature.

[43]  Renze Heidstra,et al.  The 14–Amino Acid CLV3, CLE19, and CLE40 Peptides Trigger Consumption of the Root Meristem in Arabidopsis through a CLAVATA2-Dependent Pathwayw⃞ , 2005, The Plant Cell Online.

[44]  Klaus Palme,et al.  The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots , 2005, Nature.

[45]  S. Baum,et al.  Root apical organization inArabidopsis thaliana 1. Root cap and protoderm , 1996, Protoplasma.

[46]  B. Scheres,et al.  Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division. , 2004, Genes & development.

[47]  Ari Pekka Mähönen,et al.  In planta functions of the Arabidopsis cytokinin receptor family. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[48]  H. Cho,et al.  CHRK1, a chitinase-related receptor-like kinase, interacts with NtPUB4, an armadillo repeat protein, in tobacco. , 2003, Biochimica et biophysica acta.

[49]  B. Scheres,et al.  Root-Specific CLE19 Overexpression and the sol1/2 Suppressors Implicate a CLV-like Pathway in the Control of Arabidopsis Root Meristem Maintenance , 2003, Current Biology.

[50]  P. Benfey,et al.  Intercellular movement of the putative transcription factor SHR in root patterning , 2001, Nature.

[51]  K. Shirasu,et al.  The U-box protein family in plants. , 2001, Trends in plant science.

[52]  Michele Pagano,et al.  The F-box protein family , 2000, Genome Biology.

[53]  J. Marrison,et al.  Technical advance: an aniline blue staining procedure for confocal microscopy and 3D imaging of normal and perturbed cellular phenotypes in mature Arabidopsis embryos. , 2000, The Plant journal : for cell and molecular biology.

[54]  Philip N Benfey,et al.  The SHORT-ROOT Gene Controls Radial Patterning of the Arabidopsis Root through Radial Signaling , 2000, Cell.

[55]  P. Benfey,et al.  ASYMMETRIC CELL DIVISION IN PLANTS. , 1999, Annual review of plant physiology and plant molecular biology.

[56]  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.

[57]  D. Goring,et al.  Binding of an arm repeat protein to the kinase domain of the S-locus receptor kinase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[58]  K. Gallagher,et al.  Asymmetric cell division and cell fate in plants. , 1997, Current opinion in cell biology.

[59]  Claudia van den Berg,et al.  Short-range control of cell differentiation in the Arabidopsis root meristem , 1997, Nature.

[60]  P. Benfey,et al.  The SCARECROW Gene Regulates an Asymmetric Cell Division That Is Essential for Generating the Radial Organization of the Arabidopsis Root , 1996, Cell.

[61]  C. Dean,et al.  Embryonic origin of the Arabidopsis primary root and root meristem initials , 1994 .

[62]  B. Scheres,et al.  Cellular organisation of the Arabidopsis thaliana root. , 1993, Development.

[63]  P. Benfey,et al.  Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis. , 1993, Development.