RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation.

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.

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

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.

Dynamic microtubules and endomembrane cycling contribute to polarity establishment and early development of Ectocarpus mitospores.

Many zygotes and spores of brown algae are photosensitive and establish a developmental axis in accordance with directional light cues. Ectocarpus siliculosus is being advanced as a genetic and genomic model organism for investigating brown alga development, and this report investigates photopolarization of the growth axis of mitospores. When exposed to unidirectional light, mitospores photopolarized and established a growth axis such that germination was preferentially localized to the shaded hemisphere of the spore body. The roles of the microtubule cytoskeleton and endomembrane cycling in the photopolarization process were investigated using pharmacological agents. Disruption of microtubule dynamics progressively reduced the percentage of mitospores that photopolarized, while inhibition of vesicle secretion blocked photopolarization nearly completely. Chronic treatment with these pharmacological agents severely affected algal morphogenesis. Microtubules in mitospores and algal filaments were imaged by confocal microscopy. Mitospores contained a radial microtubule array, emanating from a centrosome associated with the nuclear envelope. At germination, the radial array gradually transitioned into a longitudinal array with microtubules extending into the emerging apex. At mitosis, spindles were aligned with the growth axis of cylindrical cells in the filament, and the division plane bisected the spindle axis. These studies demonstrate that dynamic membrane cycling and microtubule assembly play fundamental roles in photopolarization and provide a foundation for future genetic and genomic investigations of this important developmental process.

Phospholipase D signaling regulates microtubule organization in the fucoid alga Silvetia compressa.

Recent studies in higher plants or animals have shown that phospholipase D (PLD) signaling regulates many aspects of development, including organization of microtubules (MTs), actin and the endomembrane system. PLD hydrolyzes structural phospholipids to form the second messenger phosphatidic acid (PA). To begin to understand the signaling pathways and molecules that regulate cytoskeletal and endomembrane arrays during early development in the brown alga, Silvetia compressa, we altered PLD activity by applying butyl alcohols to zygotes. 1-Butanol activates PLD and is a preferred substrate, primarily forming phosphatidyl butanol (P-butanol), which is not a signaling molecule. Treatment with 1-butanol inhibited cell division and cytokinesis but not photopolarization or germination, suggesting an MT-based effect. Immunolabeling revealed that 1-butanol treatment rapidly disrupted MT arrays and caused zygotes to arrest in metaphase. MT arrays recovered rapidly following butanol washout, but subsequent development depended on the timing of the treatment regime. Additionally, treatment with 1-butanol early in development disrupted endomembrane organization, known to require functional MTs. Interestingly, treatment with higher concentrations of 2-butanol, which also activates PLD, mimicked the effects of 1-butanol. In contrast, the control t-butanol had no effect on MTs or development. These results indicate that S. compressa zygotes utilize PLD signaling to regulate MT arrays. In contrast, PLD signaling does not appear to regulate actin arrays or endomembrane trafficking directly. This is the first report describing the signaling pathways that regulate cytoskeletal organization in the stramenopile (heterokont) lineage.