A Network of Local and Redundant Gene Regulation Governs Arabidopsis Seed Maturation

In Arabidopsis thaliana, four major regulators (ABSCISIC ACID INSENSITIVE3 [ABI3], FUSCA3 [FUS3], LEAFY COTYLEDON1 [LEC1], and LEC2) control most aspects of seed maturation, such as accumulation of storage compounds, cotyledon identity, acquisition of desiccation tolerance, and dormancy. The molecular basis for complex genetic interactions among these regulators is poorly understood. By analyzing ABI3 and FUS3 expression in various single, double, and triple maturation mutants, we have identified multiple regulatory links among all four genes. We found that one of the major roles of LEC2 was to upregulate FUS3 and ABI3. The lec2 mutation is responsible for a dramatic decrease in ABI3 and FUS3 expression, and most lec2 phenotypes can be rescued by ABI3 or FUS3 constitutive expression. In addition, ABI3 and FUS3 positively regulate themselves and each other, thereby forming feedback loops essential for their sustained and uniform expression in the embryo. Finally, LEC1 also positively regulates ABI3 and FUS3 in the cotyledons. Most of the genetic controls discovered were found to be local and redundant, explaining why they had previously been overlooked. This works establishes a genetic framework for seed maturation, organizing the key regulators of this process into a hierarchical network. In addition, it offers a molecular explanation for the puzzling variable features of lec2 mutant embryos.

[1]  F. Parcy,et al.  The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. , 1997, The Plant cell.

[2]  A. Wagner,et al.  Birth and death of duplicated genes in completely sequenced eukaryotes. , 2001, Trends in genetics : TIG.

[3]  D. McCarty,et al.  The Viviparous-1 developmental gene of maize encodes a novel transcriptional activator , 1991, Cell.

[4]  A. Yamamoto,et al.  LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3. , 2005, Plant & cell physiology.

[5]  H. Goodman,et al.  Isolation of the Arabidopsis ABI3 gene by positional cloning. , 1992, The Plant cell.

[6]  R. Yadegari,et al.  Plant Embryogenesis: Zygote to Seed , 1994, Science.

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

[8]  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.

[9]  U. Wobus,et al.  Seed maturation: genetic programmes and control signals. , 1999, Current opinion in plant biology.

[10]  T. Lynch,et al.  Regulation and Role of the Arabidopsis Abscisic Acid-Insensitive 5 Gene in Abscisic Acid, Sugar, and Stress Response1 , 2002, Plant Physiology.

[11]  P. McCourt,et al.  A regulatory role for the ABI3 gene in the establishment of embryo maturation in Arabidopsis thaliana , 1995 .

[12]  I. Díaz,et al.  Synergistic Activation of Seed Storage Protein Gene Expression in Arabidopsis by ABI3 and Two bZIPs Related to OPAQUE2* , 2003, Journal of Biological Chemistry.

[13]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

[14]  P. Herrmann,et al.  FUSCA3 encodes a protein with a conserved VP1/ABI3-like B3 domain which is of functional importance for the regulation of seed maturation in Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[15]  Thomas Kroj,et al.  Regulation of storage protein gene expression in Arabidopsis , 2003, Development.

[16]  fusca3: A Heterochronic Mutation Affecting Late Embryo Development in Arabidopsis. , 1994, The Plant cell.

[17]  M. Koornneef,et al.  Sequential steps for developmental arrest in Arabidopsis seeds. , 2001, Development.

[18]  Satoshi Naito,et al.  The FUS3 transcription factor functions through the epidermal regulator TTG1 during embryogenesis in Arabidopsis. , 2004, The Plant journal : for cell and molecular biology.

[19]  Mads Kærn,et al.  Noise in eukaryotic gene expression , 2003, Nature.

[20]  U. Wobus,et al.  The FUS3 gene of Arabidopsis thaliana is a regulator of gene expression during late embryogenesis , 1994 .

[21]  T. Steeves.  The evolution and biological significance of seeds , 1983 .

[22]  L. Lepiniec,et al.  LEAFY COTYLEDON 2 activation is sufficient to trigger the accumulation of oil and seed specific mRNAs in Arabidopsis leaves , 2005, FEBS letters.

[23]  Farren J. Isaacs,et al.  Prediction and measurement of an autoregulatory genetic module , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Erich Bornberg-Bauer,et al.  Convergent evolution of gene networks by single‐gene duplications in higher eukaryotes , 2004, EMBO reports.

[25]  M. Delseny,et al.  Differential expression of the Arabidopsis genes coding for Em-like proteins. , 2000, Journal of experimental botany.

[26]  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.

[27]  R. Sommer,et al.  The evolution of developmental mechanisms. , 2003, Developmental biology.

[28]  E. Davidson,et al.  Gene regulatory networks for development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[29]  S. Naito,et al.  The role of ABI3 and FUS3 loci in Arabidopsis thaliana on phase transition from late embryo development to germination. , 2000, Developmental biology.

[30]  M. Thattai,et al.  Intrinsic noise in gene regulatory networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  S. Teichmann,et al.  Gene regulatory network growth by duplication , 2004, Nature Genetics.

[32]  P. Herrmann,et al.  FUSCA3 encodes a protein with a conserved VP1/AB13-like B3 domain which is of functional importance for the regulation of seed maturation in Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[33]  D. Meinke.  A Homoeotic Mutant of Arabidopsis thaliana with Leafy Cotyledons , 1992, Science.

[34]  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.

[35]  Jesús Vicente-Carbajosa,et al.  Seed maturation: developing an intrusive phase to accomplish a quiescent state. , 2005, The International journal of developmental biology.

[36]  M. West,et al.  LEAFY COTYLEDON1 Is an Essential Regulator of Late Embryogenesis and Cotyledon Identity in Arabidopsis. , 1994, The Plant cell.

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

[38]  M. Delseny,et al.  Changes in gene expression in the leafy cotyledon1 (lec1) and fusca3 (fus3) mutants of Arabidopsis thaliana L. , 2000, Journal of experimental botany.

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

[40]  L. Hood,et al.  Regulatory gene networks and the properties of the developmental process , 2003, Proceedings of the National Academy of Sciences of the United States of America.