The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis1[OPEN]

BBM and other AIL transcription factors induce somatic embryogenesis in a dose- and context-dependent mechanism and through direct transcriptional regulation of major embryo identity genes. Somatic embryogenesis is an example of induced cellular totipotency, where embryos develop from vegetative cells rather than from gamete fusion. Somatic embryogenesis can be induced in vitro by exposing explants to growth regulators and/or stress treatments. The BABY BOOM (BBM) and LEAFY COTYLEDON1 (LEC1) and LEC2 transcription factors are key regulators of plant cell totipotency, as ectopic overexpression of either transcription factor induces somatic embryo formation from Arabidopsis (Arabidopsis thaliana) seedlings without exogenous growth regulators or stress treatments. Although LEC and BBM proteins regulate the same developmental process, it is not known whether they function in the same molecular pathway. We show that BBM transcriptionally regulates LEC1 and LEC2, as well as the two other LAFL genes, FUSCA3 (FUS3) and ABSCISIC ACID INSENSITIVE3 (ABI3). LEC2 and ABI3 quantitatively regulate BBM-mediated somatic embryogenesis, while FUS3 and LEC1 are essential for this process. BBM-mediated somatic embryogenesis is dose and context dependent, and the context-dependent phenotypes are associated with differential LAFL expression. We also uncover functional redundancy for somatic embryogenesis among other Arabidopsis BBM-like proteins and show that one of these proteins, PLETHORA2, also regulates LAFL gene expression. Our data place BBM upstream of other major regulators of plant embryo identity and totipotency.

[1]  P. McCourt,et al.  A screen for genes that function in abscisic acid signaling in Arabidopsis thaliana. , 2002, Genetics.

[2]  M. Gaj.  Factors Influencing Somatic Embryogenesis Induction and Plant Regeneration with Particular Reference to Arabidopsis thaliana (L.) Heynh , 2004, Plant Growth Regulation.

[3]  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.

[4]  So-Young Park,et al.  Bioreactor Culture of Shoots and Somatic Embryos of Medicinal Plants for Production of Bioactive Compounds , 2014 .

[5]  G. Angenent,et al.  ASYMMETRIC LEAVES2-LIKE1gene, a member of the AS2/LOB family, controls proximal–distal patterning in Arabidopsis petals , 2005, Plant Molecular Biology.

[6]  J. Mu,et al.  Arabidopsis transcription factor genes NF-YA1, 5, 6, and 9 play redundant roles in male gametogenesis, embryogenesis, and seed development. , 2013, Molecular plant.

[7]  S. E. Perry,et al.  Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development1[C][W][OA] , 2013, Plant Physiology.

[8]  E. Meyerowitz,et al.  PLETHORA Genes Control Regeneration by a Two-Step Mechanism , 2015, Current Biology.

[9]  V. Sharma,et al.  Ectopic Expression of BABY BOOM Triggers a Conversion from Vegetative to Embryonic Growth Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001941. , 2002, The Plant Cell Online.

[10]  B. Krizek,et al.  Three Arabidopsis AIL/PLT genes act in combination to regulate shoot apical meristem function. , 2012, The Plant journal : for cell and molecular biology.

[11]  L. Lepiniec,et al.  LEAFY COTYLEDON2 encodes a B3 domain transcription factor that induces embryo development , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[12]  B. Krizek,et al.  AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or division-competent states , 2005, Plant Molecular Biology.

[13]  D. Soltis,et al.  Phylogeny and domain evolution in the APETALA2-like gene family. , 2006, Molecular biology and evolution.

[14]  F. Parcy,et al.  Interactions between the ABI1 and the ectopically expressed ABI3 genes in controlling abscisic acid responses in Arabidopsis vegetative tissues. , 1997, The Plant journal : for cell and molecular biology.

[15]  B. Krizek,et al.  DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. , 2000, Nucleic acids research.

[16]  Masanori Okamoto,et al.  The transcription factor FUSCA3 controls developmental timing in Arabidopsis through the hormones gibberellin and abscisic acid. , 2004, Developmental cell.

[17]  B. Krizek,et al.  AINTEGUMENTA and AINTEGUMENTA-LIKE6 Act Redundantly to Regulate Arabidopsis Floral Growth and Patterning1[C][W][OA] , 2009, Plant Physiology.

[18]  B. Krizek.  Ectopic expression of AINTEGUMENTA in Arabidopsis plants results in increased growth of floral organs. , 1999, Developmental genetics.

[19]  C. Somerville,et al.  PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Stijn Dhondt,et al.  Arabidopsis Class I and Class II TCP Transcription Factors Regulate Jasmonic Acid Metabolism and Leaf Development Antagonistically1[C][W] , 2012, Plant Physiology.

[21]  Gabino Sanchez-Perez,et al.  AIL and HDG proteins act antagonistically to control cell proliferation , 2015, Development.

[22]  Wayne R Curtis,et al.  Enhanced somatic embryogenesis in Theobroma cacao using the homologous BABY BOOM transcription factor , 2015, BMC Plant Biology.

[23]  Jenny Banh,et al.  Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation[OPEN] , 2016, Plant Cell.

[24]  A. Schier,et al.  Morphogen gradients: from generation to interpretation. , 2011, Annual review of cell and developmental biology.

[25]  K. Torii,et al.  Arabidopsis homeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis , 2013, Development.

[26]  D. Meinke,et al.  Leafy Cotyledon Mutants of Arabidopsis. , 1994, The Plant cell.

[27]  S. E. Perry,et al.  Expression and Maintenance of Embryogenic Potential Is Enhanced through Constitutive Expression of AGAMOUS-Like 151 , 2003, Plant Physiology.

[28]  Y. Kamiya,et al.  CHOTTO1, a Putative Double APETALA2 Repeat Transcription Factor, Is Involved in Abscisic Acid-Mediated Repression of Gibberellin Biosynthesis during Seed Germination in Arabidopsis1[W][OA] , 2009, Plant Physiology.

[29]  Alexandra To,et al.  A Network of Local and Redundant Gene Regulation Governs Arabidopsis Seed Maturation , 2006, The Plant Cell Online.

[30]  R. Amasino,et al.  The PLETHORA Genes Mediate Patterning of the Arabidopsis Root Stem Cell Niche , 2004, Cell.

[31]  S. D. Rider,et al.  PICKLE Acts throughout the Plant to Repress Expression of Embryonic Traits and May Play a Role in Gibberellin-Dependent Responses1 , 2004, Plant Physiology.

[32]  Masaharu Suzuki,et al.  Repression of the LEAFY COTYLEDON 1/B3 Regulatory Network in Plant Embryo Development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 Genes1[C][W] , 2006, Plant Physiology.

[33]  B. Krizek.  AINTEGUMENTA-LIKE genes have partly overlapping functions with AINTEGUMENTA but make distinct contributions to Arabidopsis thaliana flower development , 2015, Journal of experimental botany.

[34]  J. Dunwell,et al.  Overexpression of coconut AINTEGUMENTA-like gene, CnANT, promotes in vitro regeneration in transgenic Arabidopsis , 2013, Plant Cell, Tissue and Organ Culture (PCTOC).

[35]  W. Muir,et al.  Identification of targets of PICKLE 2 The CHD 3 remodeler PICKLE associates with genes enriched for trimethylation of histone H 3 lysine 27 , 2012 .

[36]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[37]  M. Stitt,et al.  Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w] , 2005, Plant Physiology.

[38]  J. Harada,et al.  LECs go crazy in embryo development. , 2008, Trends in plant science.

[39]  G. Angenent,et al.  Plasticity in Cell Division Patterns and Auxin Transport Dependency during in Vitro Embryogenesis in Brassica napus[C][W] , 2014, Plant Cell.

[40]  H. Edenberg,et al.  Coordinate repression of regulators of embryonic identity by PICKLE during germination in Arabidopsis. , 2003, The Plant journal : for cell and molecular biology.

[41]  W. Deng,et al.  A novel method for induction of plant regeneration via somatic embryogenesis , 2009 .

[42]  Edwin Cuppen,et al.  The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots[OPEN] , 2016, Plant Cell.

[43]  M. Eaddy,et al.  AINTEGUMENTA-LIKE6 regulates cellular differentiation in flowers , 2012, Plant Molecular Biology.

[44]  A. Azhagiri,et al.  Transplastomics in Arabidopsis: progress toward developing an efficient method. , 2011, Methods in molecular biology.

[45]  F. Parcy,et al.  Regulation of gene expression programs during Arabidopsis seed development: roles of the ABI3 locus and of endogenous abscisic acid. , 1994, The Plant cell.

[46]  G. Angenent,et al.  Efficient sweet pepper transformation mediated by the BABY BOOM transcription factor , 2011, Plant Cell Reports.

[47]  J. Tregear,et al.  EgAP2-1, an AINTEGUMENTA-like (AIL) gene expressed in meristematic and proliferating tissues of embryos in oil palm , 2007, Planta.

[48]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[49]  J. Keilwagen,et al.  Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon , 2012, Nucleic acids research.

[50]  S. Takeda,et al.  Diverse roles and mechanisms of gene regulation by the Arabidopsis seed maturation master regulator FUS3 revealed by microarray analysis. , 2010, Plant & cell physiology.

[51]  J. A. Teixeira da Silva,et al.  Synseed technology-a complete synthesis. , 2013, Biotechnology advances.

[52]  Aiming Wang,et al.  Molecular regulation of plant somatic embryogenesis , 2013, In Vitro Cellular & Developmental Biology - Plant.

[53]  S. Yokoi,et al.  Arabidopsis EMBRYOMAKER encoding an AP2 domain transcription factor plays a key role in developmental change from vegetative to embryonic phase , 2010, Plant Molecular Biology.

[54]  J. Keilwagen,et al.  Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana. , 2012, The Plant journal : for cell and molecular biology.

[55]  A. Stromberg,et al.  Global Identification of Targets of the Arabidopsis MADS Domain Protein AGAMOUS-Like15[C][W] , 2009, The Plant Cell Online.

[56]  T. Soliman,et al.  Identification and functional analysis of BABY BOOM genes from Rosa canina , 2014, Biologia Plantarum.

[57]  Robert B Goldberg,et al.  Arabidopsis LEAFY COTYLEDON1 Is Sufficient to Induce Embryo Development in Vegetative Cells , 1998, Cell.

[58]  Masaharu Suzuki,et al.  Distinct Roles of LAFL Network Genes in Promoting the Embryonic Seedling Fate in the Absence of VAL Repression1[W][OPEN] , 2013, Plant Physiology.

[59]  B. Baum,et al.  Control of somatic embryogenesis and embryo development by AP2 transcription factors , 2010, Plant Molecular Biology.

[60]  Renze Heidstra,et al.  PLETHORA proteins as dose-dependent master regulators of Arabidopsis root development , 2007, Nature.

[61]  V. Willemsen,et al.  AINTEGUMENTA-LIKE proteins: hubs in a plethora of networks. , 2014, Trends in plant science.

[62]  F. Berger,et al.  Complementation of Seed Maturation Phenotypes by Ectopic Expression of ABSCISIC ACID INSENSITIVE3, FUSCA3 and LEAFY COTYLEDON2 in Arabidopsis. , 2015, Plant & cell physiology.

[63]  W. Muir,et al.  The CHD3 Remodeler PICKLE Associates with Genes Enriched for Trimethylation of Histone H3 Lysine 271[W][OA] , 2012, Plant Physiology.

[64]  A. Fehér.  Somatic embryogenesis - Stress-induced remodeling of plant cell fate. , 2015, Biochimica et biophysica acta.

[65]  Mathew G. Lewsey,et al.  Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape , 2016, Cell.

[66]  G. Ingram,et al.  AtDEK1 is essential for specification of embryonic epidermal cell fate. , 2005, The Plant journal : for cell and molecular biology.

[67]  C. Maliepaard,et al.  BABY BOOM target genes provide diverse entry points into cell proliferation and cell growth pathways , 2008, Plant Molecular Biology.

[68]  Masaharu Suzuki,et al.  Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks , 2014, Wiley interdisciplinary reviews. Developmental biology.

[69]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[70]  P. Fobert,et al.  High-level expression of sugar inducible gene2 (HSI2) is a negative regulator of drought stress tolerance in Arabidopsis , 2013, BMC Plant Biology.

[71]  L. Pâques,et al.  Somatic embryogenesis in forestry with a focus on Europe: state-of-the-art, benefits, challenges and future direction , 2013, Tree Genetics & Genomes.

[72]  Y. Kamiya,et al.  CHOTTO 1 , a Putative Double APETALA 2 Repeat Transcription Factor , Is Involved in Abscisic Acid-Mediated Repression of Gibberellin Biosynthesis during Seed Germination in Arabidopsis 1 [ W ] [ OA ] , 2009 .

[73]  L. Iyer,et al.  Gene Networks and Chromatin and Transcriptional Regulation of the Phaseolin Promoter in Arabidopsis[C][W] , 2013, Plant Cell.

[74]  Keqiang Wu,et al.  HISTONE DEACETYLASE19 Interacts with HSL1 and Participates in the Repression of Seed Maturation Genes in Arabidopsis Seedlings[C][W] , 2013, Plant Cell.

[75]  Robert B Goldberg,et al.  Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.