title: Meta-Analysis of Arabidopsis KANADI1 Direct Target Genes Identifies a Basic Growth-Promoting Module Acting Upstream of Hormonal Signaling Pathways.
abstract: An intricate network of antagonistically acting transcription factors mediates the formation of a flat leaf lamina of Arabidopsis (Arabidopsis thaliana) plants. In this context, members of the class III homeodomain leucine zipper (HD-ZIPIII) transcription factor family specify the adaxial domain (future upper side) of the leaf, while antagonistically acting KANADI transcription factors determine the abaxial domain (future lower side). Here, we used a messenger RNA sequencing approach to identify genes regulated by KANADI1 (KAN1) and subsequently performed a meta-analysis combining our data sets with published genome-wide data sets. Our analysis revealed that KAN1 acts upstream of several genes encoding auxin biosynthetic enzymes. When exposed to shade, we found three YUCCA genes, YUC2, YUC5, and YUC8, to be transcriptionally up-regulated, which correlates with an increase in the levels of free auxin. When ectopically expressed, KAN1 is able to transcriptionally repress these three YUC genes and thereby block shade-induced auxin biosynthesis. Consequently, KAN1 is able to strongly suppress shade-avoidance responses. Taken together, we hypothesize that HD-ZIPIII/KAN form the basis of a basic growth-promoting module. Hypocotyl extension in the shade and outgrowth of new leaves both involve auxin synthesis and signaling, which are under the direct control of HD-ZIPIII/KAN.
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.).
authors.forename: Yakun
authors.identifier: http://orcid.org/0000-0003-1943-9577
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.).
authors.forename: Daniel
authors.identifier: http://orcid.org/0000-0002-2553-0660
authors.initials: D
authors.lastname: Straub
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.).
authors.forename: Tenai
authors.initials: T
authors.lastname: Eguen
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.).
authors.forename: Ronny
authors.initials: R
authors.lastname: Brandt
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.).
authors.forename: Mark
authors.initials: M
authors.lastname: Stahl
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.).
authors.forename: Jaime F
authors.identifier: http://orcid.org/0000-0003-1516-0341
authors.initials: JF
authors.lastname: Martínez-García
authors.affiliation: Centre for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany (Y.X., D.S., T.E., M.S., S.W.);Copenhagen Plant Science Centre, Department for Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark (D.S., T.E., S.W.);Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany (R.B.);Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain (J.F.M.-G.); andInstitució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain (J.F.M.-G.) wenkel@plen.ku.dk.
authors.forename: Stephan
authors.identifier: http://orcid.org/0000-0001-5764-9423
authors.initials: S
authors.lastname: Wenkel
mesh_terms: D017360:Arabidopsis / Q000254:growth & development / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism*; D018744:DNA, Plant / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D007210:Indoleacetic Acids / Q000378:metabolism*; D006899:Mixed Function Oxygenases / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D012045:Regulatory Sequences, Nucleic Acid; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D007210:Indoleacetic Acids; C430846:KANADI protein, Arabidopsis; D014157:Transcription Factors; D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; C000609125:YUC5 protein, Arabidopsis; C000608861:YUCCA2 protein, Arabidopsis; C585335:YUCCA8 protein, Arabidopsis