Alan Lloyd

AGL80 Is Required for Central Cell and Endosperm Development in Arabidopsis

During plant reproduction, the central cell of the female gametophyte becomes fertilized to produce the endosperm, a storage tissue that nourishes the developing embryo within the seed. The molecular mechanisms controlling the specification and differentiation of the central cell are poorly understood. We identified a female gametophyte mutant in Arabidopsis thaliana, fem111, that is affected in central cell development. In fem111 female gametophytes, the central cells nucleolus and vacuole fail to mature properly. In addition, endosperm development is not initiated after fertilization of fem111 female gametophytes. fem111 contains a T-DNA insertion in AGAMOUS-LIKE80 (AGL80). FEM111/AGL80 is a member of the MADS box family of genes that likely encode transcription factors. An AGL80–green fluorescent protein fusion protein is localized to the nucleus. Within the ovule and seed, FEM111/AGL80 is expressed exclusively in the central cell and uncellularized endosperm. FEM111/AGL80 expression is also detected in roots, leaves, floral stems, anthers, and young flowers by real-time RT-PCR. FEM111/AGL80 is required for the expression of two central cell–expressed genes, DEMETER and DD46, but not for a third central cell–expressed gene, FERTILIZATION-INDEPENDENT SEED2. Together, these data suggest that FEM111/AGL80 functions as a transcription factor within the central cell gene regulatory network and controls the expression of downstream genes required for central cell development and function.

The AGL62 MADS Domain Protein Regulates Cellularization during Endosperm Development in Arabidopsis

Endosperm, a storage tissue in the angiosperm seed, provides nutrients to the embryo during seed development and/or to the developing seedling during germination. A major event in endosperm development is the transition between the syncytial phase, during which the endosperm nuclei undergo many rounds of mitosis without cytokinesis, and the cellularized phase, during which cell walls form around the endosperm nuclei. The molecular processes controlling this phase transition are not understood. In agl62 seeds, the endosperm cellularizes prematurely, indicating that AGL62 is required for suppression of cellularization during the syncytial phase. AGL62 encodes a Type I MADS domain protein that likely functions as a transcription factor. During seed development, AGL62 is expressed exclusively in the endosperm. During wild-type endosperm development, AGL62 expression is strong during the syncytial phase and then declines abruptly just before cellularization. By contrast, in mutant seeds containing defects in some FERTILIZATION-INDEPENDENT SEED (FIS) class Polycomb group genes, the endosperm fails to cellularize and AGL62 expression fails to decline. Together, these data suggest that AGL62 suppresses cellularization during the syncytial phase of endosperm development and that endosperm cellularization is triggered via direct or indirect AGL62 inactivation by the FIS polycomb complex.

AGL61 Interacts with AGL80 and Is Required for Central Cell Development in Arabidopsis

The central cell of the female gametophyte plays a role in pollen tube guidance and in regulating the initiation of endosperm development. Following fertilization, the central cell gives rise to the seeds endosperm, which nourishes the developing embryo within the seed. The molecular mechanisms controlling specification and differentiation of the central cell are poorly understood. We identified AGL61 in a screen for transcription factor genes expressed in the female gametophyte. AGL61 encodes a Type I MADS domain protein, which likely functions as a transcription factor. Consistent with this, an AGL61-green fluorescent protein fusion protein is localized to the nucleus. In the context of the ovule and seed, AGL61 is expressed exclusively in the central cell and early endosperm. agl61 female gametophytes are affected in the central cell specifically. The morphological defects include an overall reduction in size of the central cell and a reduced or absent central cell vacuole. When fertilized with wild-type pollen, agl61 central cells fail to give rise to endosperm. In addition, synergid- and antipodal-expressed genes are ectopically expressed in agl61 central cells. The expression pattern and mutant phenotype of AGL61 are similar to those of AGL80, suggesting that AGL61 may function as a heterodimer with AGL80 within the central cell; consistent with this, AGL61 and AGL80 interact in yeast two-hybrid assays. Together, these data suggest that AGL61 functions as a transcription factor and controls the expression of downstream genes during central cell development.

NUCLEAR FUSION DEFECTIVE1 Encodes the Arabidopsis RPL21M Protein and Is Required for Karyogamy during Female Gametophyte Development and Fertilization

Karyogamy, or nuclear fusion, is essential for sexual reproduction. In angiosperms, karyogamy occurs three times: twice during double fertilization of the egg cell and the central cell and once during female gametophyte development when the two polar nuclei fuse to form the diploid central cell nucleus. The molecular mechanisms controlling karyogamy are poorly understood. We have identified nine female gametophyte mutants in Arabidopsis (Arabidopsis thaliana), nuclear fusion defective1 (nfd1) to nfd9, that are defective in fusion of the polar nuclei. In the nfd1 to nfd6 mutants, failure of fusion of the polar nuclei is the only defect detected during megagametogenesis. nfd1 is also affected in karyogamy during double fertilization. Using transmission electron microscopy, we showed that nfd1 nuclei fail to undergo fusion of the outer nuclear membranes. nfd1 contains a T-DNA insertion in RPL21M that is predicted to encode the mitochondrial 50S ribosomal subunit L21, and a wild-type copy of this gene rescues the mutant phenotype. Consistent with the predicted function of this gene, an NFD1-green fluorescent protein fusion protein localizes to mitochondria and the NFD1/RPL21M gene is expressed throughout the plant. The nfd3, nfd4, nfd5, and nfd6 mutants also contain T-DNA insertions in genes predicted to encode proteins that localize to mitochondria, suggesting a role for this organelle in nuclear fusion.

RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

RNA profiling of maize kernel compartments revealed coexpression modules for each major cell type in the endosperm, including a module regulating differentiation of the basal endosperm transfer layer. Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the genetic networks that regulate endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the maize (Zea mays) kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene coexpression network analysis identified coexpression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a coexpression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types.

Characterization of two Drosophila POU domain genes, related to oct-1 and oct-2, and the regulation of their expression patterns

We have characterized two genes from Drosophila melanogaster that encode proteins with POU domains showing a high degree of identity with the human Oct-1 and Oct-2 transcription factors. These POU domain genes, pdm-1 and pdm-2, are expressed at high levels during early embryogenesis and at lower levels throughout the rest of development. Both genes are expressed as two stripes in the presumptive abdominal region during the blastoderm stage, followed by thirteen stripes in the germ band extended stage. This pattern of expression is altered in mutants for a gap gene (hunchback) and a pair-rule gene (fushi tarazu). In later stage embryos, both pdm-1 and pdm-2 are expressed in selected neuroblasts in the ventral nervous system, with higher levels in the three thoracic segments and lower levels in the abdominal segments. The low level of expression in the abdominal segments is maintained by the genes within the bithorax complex (BX-C). We have also identified the cells in the dorsal and lateral clusters of the peripheral nervous system that express pdm-1 and pdm-2, and show that some of these cells derive from lineages that require BX-C functions. Together, these results suggest that previously characterized members of the embryonic regulatory hierarchy specify the patterns of the POU domain gene expression, which, in turn, function during neurogenesis and perhaps in earlier stages.

Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing

Significance In flowering plants, double fertilization gives rise to an embryo and the endosperm, an absorptive storage structure that supports embryogenesis and seedling germination. In cereal grains, endosperm comprises a large proportion of the mature seed, contains large amounts of carbohydrates and proteins, and is an important source of food, feed, and industrial raw materials. This study provides a comprehensive profile of the genes expressed in the early developing endosperm in maize. We also show how a series of temporal programs of gene expression correlate with progressive functional and cellular specializations. Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development and seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed, and renewable resources. Little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step toward understanding these networks, we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination. Analysis of these gene sets identified temporal programs of gene expression, including hundreds of transcription-factor genes. We found a close correlation of the sequentially expressed gene sets with distinct cellular and metabolic programs in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemporal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality.

The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98

The female gametophyte contains two synergid cells that play a role in many steps of the angiosperm reproductive process, including pollen tube guidance. At their micropylar poles, the synergid cells have a thickened and elaborated cell wall: the filiform apparatus that is thought to play a role in the secretion of the pollen tube attractant(s). MYB98 regulates an important subcircuit of the synergid gene regulatory network (GRN) that functions to activate the expression of genes required for pollen tube guidance and filiform apparatus formation. The MYB98 subcircuit comprises at least 83 downstream genes, including 48 genes within four gene families (CRP810, CRP3700, CRP3730 and CRP3740) that encode Cys-rich proteins. We show that the 11 CRP3700 genes, which include DD11 and DD18, are regulated by a common cis-element, GTAACNT, and that a multimer of this sequence confers MYB98-dependent synergid expression. The GTAACNT element contains the MYB98-binding site identified in vitro, suggesting that the 11 CRP3700 genes are direct targets of MYB98. We also show that five of the CRP810 genes, which include DD2, lack a functional GTAACNT element, suggesting that they are not directly regulated by MYB98. In addition, we show that the five CRP810 genes are regulated by the cis-element AACGT, and that a multimer of this sequence confers synergid expression. Together, these results suggest that the MYB98 branch of the synergid GRN is multi-tiered and, therefore, contains at least one additional downstream transcription factor.

SUPPRESSOR OF FRIGIDA (SUF4) supports gamete fusion via regulating arabidopsis EC1 gene expression

In Arabidopsis, gamete fusion requires the C2H2 transcription factor SUF4, which regulates the expression of the EGG CELL1 gene family. The EGG CELL1 (EC1) gene family of Arabidopsis (Arabidopsis thaliana) comprises five members that are specifically expressed in the egg cell and redundantly control gamete fusion during double fertilization. We investigated the activity of all five EC1 promoters in promoter-deletion studies and identified SUF4 (SUPPRESSOR OF FRIGIDA4), a C2H2 transcription factor, as a direct regulator of the EC1 gene expression. In particular, we demonstrated that SUF4 binds to all five Arabidopsis EC1 promoters, thus regulating their expression. The down-regulation of SUF4 in homozygous suf4-1 ovules results in reduced EC1 expression and delayed sperm fusion, which can be rescued by expressing SUF4-β-glucuronidase under the control of the SUF4 promoter. To identify more gene products able to regulate EC1 expression together with SUF4, we performed coexpression studies that led to the identification of MOM1 (MORPHEUS’ MOLECULE1), a component of a silencing mechanism that is independent of DNA methylation marks. In mom1-3 ovules, both SUF4 and EC1 genes are down-regulated, and EC1 genes show higher levels of histone 3 lysine-9 acetylation, suggesting that MOM1 contributes to the regulation of SUF4 and EC1 gene expression.

Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm

Genome-wide analysis of genes regulated by the maize transcription factor Opaque-2 uncovered its functions in regulation of cell differentiation and endosperm storage development. Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products, and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize (Zea mays) bZIP transcription factor Opaque-2 (O2). Here, we mapped in vivo binding sites of O2 in B73 endosperm and compared the results with genes differentially expressed in B73 and B73o2. We identified 186 putative direct O2 targets and 1677 indirect targets, encoding a broad set of gene functionalities. Examination of the temporal expression patterns of O2 targets revealed at least two distinct modes of O2-mediated gene activation. Two O2-activated genes, bZIP17 and NAKED ENDOSPERM2 (NKD2), encode transcription factors, which can in turn coactivate other O2 network genes with O2. NKD2 (with its paralog NKD1) was previously shown to be involved in regulation of aleurone development. Collectively, our results provide insights into the complexity of the O2-regulated network and its role in regulation of endosperm cell differentiation and function.