RESUMEN
Chromatin is dynamically modified throughout the plant life cycle to regulate gene expression in response to environmental and developmental cues. Although such epigenetic information can be inherited across generations in plants, chromatin features that regulate gene expression are typically reprogrammed during plant gametogenesis and directly after fertilization. Nevertheless, environmentally induced epigenetic marks on genes can be transmitted across generations. Moreover, epigenetic information installed on early embryonic chromatin can be stably inherited during subsequent growth and influence how plants respond to environmental conditions much later in development. Here, we review recent breakthroughs towards deciphering mechanisms underlying epigenetic reprogramming and transcriptional priming during early plant embryogenesis.
Asunto(s)
Epigénesis Genética , Regulación de la Expresión Génica de las Plantas , Semillas/genética , Semillas/crecimiento & desarrollo , Cromatina/metabolismo , Cromatina/genética , Desarrollo de la Planta/genética , Plantas/genética , Plantas/metabolismoRESUMEN
As plant research generates an ever-growing volume of spatial quantitative data, the need for decentralized and user-friendly visualization tools to explore large and complex datasets becomes crucial. Existing resources, such as the Plant eFP (electronic Fluorescent Pictograph) viewer, have played a pivotal role on the communication of gene expression data across many plant species. However, although widely used by the plant research community, the Plant eFP viewer lacks open and user-friendly tools for the creation of customized expression maps independently. Plant biologists with less coding experience can often encounter challenges when attempting to explore ways to communicate their own spatial quantitative data. We present 'ggPlantmap' an open-source R package designed to address this challenge by providing an easy and user-friendly method for the creation of ggplot representative maps from plant images. ggPlantmap is built in R, one of the most used languages in biology, to empower plant scientists to create and customize eFP-like viewers tailored to their experimental data. Here, we provide an overview of the package and tutorials that are accessible even to users with minimal R programming experience. We hope that ggPlantmap can assist the plant science community, fostering innovation, and improving our understanding of plant development and function.
Asunto(s)
Plantas , Programas Informáticos , Plantas/metabolismo , Procesamiento de Imagen Asistido por Computador/métodosRESUMEN
The LEAFY COTYLEDON1 (LEC1) transcription factor is a central regulator of seed development, because it controls diverse biological programs during seed development, such as embryo morphogenesis, photosynthesis, and seed maturation. To understand how LEC1 regulates different gene sets during development, we explored the possibility that LEC1 acts in combination with other transcription factors. We identified and compared genes that are directly transcriptionally regulated by ABA-RESPONSIVE ELEMENT BINDING PROTEIN3 (AREB3), BASIC LEUCINE ZIPPER67 (bZIP67), and ABA INSENSITIVE3 (ABI3) with those regulated by LEC1. We showed that LEC1 operates with specific sets of transcription factors to regulate different gene sets and, therefore, distinct developmental processes. Thus, LEC1 controls diverse processes through its combinatorial interactions with other transcription factors. DNA binding sites for the transcription factors are closely clustered in genomic regions upstream of target genes, defining cis-regulatory modules that are enriched for DNA sequence motifs that resemble sequences known to be bound by these transcription factors. Moreover, cis-regulatory modules for genes regulated by distinct transcription factor combinations are enriched for different sets of DNA motifs. Expression assays with embryo cells indicate that the enriched DNA motifs are functional cis elements that regulate transcription. Together, the results suggest that combinatorial interactions between LEC1 and other transcription factors are mediated by cis-regulatory modules containing clustered cis elements and by physical interactions that are documented to occur between the transcription factors.
Asunto(s)
Proteínas Potenciadoras de Unión a CCAAT/metabolismo , Glycine max/crecimiento & desarrollo , Glycine max/metabolismo , Semillas/crecimiento & desarrollo , Factores de Transcripción/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Sitios de Unión , Proteínas Potenciadoras de Unión a CCAAT/genética , Proteínas de Unión al ADN , Regulación de la Expresión Génica de las Plantas , Motivos de Nucleótidos , Desarrollo de la Planta/genética , Desarrollo de la Planta/fisiología , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , ARN Mensajero , Glycine max/embriología , Glycine max/genética , Factores de Transcripción/genéticaRESUMEN
Seed development is a complex period of the flowering plant life cycle. After fertilization, the three main regions of the seed, embryo, endosperm and seed coat, undergo a series of developmental processes that result in the production of a mature seed that is developmentally arrested, desiccated, and metabolically quiescent. These processes are highly coordinated, both temporally and spatially, to ensure the proper growth and development of the seed. The transcription factor, LEAFY COTYLEDON1 (LEC1), is a central regulator that controls several aspects of embryo and endosperm development, including embryo morphogenesis, photosynthesis, and storage reserve accumulation. Thus, LEC1 regulates distinct sets of genes at different stages of seed development. Despite its critical importance for seed development, an understanding of the mechanisms underlying LEC1's multifunctionality is only beginning to be obtained. Recent studies describe the roles of specific transcription factors and the hormones, gibberellic acid and abscisic acid, in controlling the activity and transcriptional specificity of LEC1 across seed development. Moreover, studies indicate that LEC1 acts as a pioneer transcription factor to promote epigenetic reprogramming during embryogenesis. In this review, we discuss the mechanisms that enable LEC1 to serve as a central regulator of seed development.
Asunto(s)
Proteínas de Arabidopsis/metabolismo , Semillas/metabolismo , Semillas/fisiología , Factores de Transcripción/metabolismo , Ácido Abscísico/metabolismo , Arabidopsis/metabolismo , Arabidopsis/fisiología , Proteínas de Arabidopsis/genética , Proteínas Potenciadoras de Unión a CCAAT/genética , Proteínas Potenciadoras de Unión a CCAAT/metabolismo , Regulación de la Expresión Génica de las Plantas/genética , Regulación de la Expresión Génica de las Plantas/fisiología , Giberelinas/metabolismo , Hojas de la Planta/metabolismo , Hojas de la Planta/fisiología , Semillas/genética , Factores de Transcripción/genéticaRESUMEN
Somatic embryogenesis is an important biotechnological tool in the large-scale propagation of elite genotypes and ex situ conservation of conifer species. Protocols for the induction and proliferation of embryogenic cultures (ECs) of Brazilian pine (Araucaria angustifolia (Bert.) O. Ktze) are well established, although the proper formation of mature somatic embryos (SEs) is still problematic. Thus, the identification of molecular markers for the screening of ECs able to respond to maturation conditions (abscisic acid and osmotic agents) is highly desirable. To develop molecular markers for the early detection of ECs able to develop well-formed SEs under maturation conditions, we analyzed the proteins found during the proliferation phase of A. angustifolia cell lines with different embryogenic capabilities, with one cell line being responsive to maturation conditions (R cell line), and one cell line that presented blocked development of SEs (B cell line). In addition, based on the peptides identified, polyamine levels (free and conjugate), ethylene production and reactive oxygen species (ROS) emission were analyzed using both EC lines (R and B cell lines). A marked difference in the biochemistry of ECs between these two cell lines was observed. Eleven proteins that were differentially expressed in the cell lines were identified by the combination of two-dimensional electrophoresis (2-DE) and MALDI-TOF/TOF mass spectrometry. Among these, S-adenosylmethionine synthase, the enzyme associated with polyamines and ethylene biosynthesis, was observed exclusively in the R cell line, while a protein linked to the oxidative stress subunit F of NADH dehydrogenase was observed exclusively in the B cell lines. Additionally, B cell lines showed higher levels of diamine putrescine and lower levels of ethylene. Higher values of ethylene and ROS were observed for the cell line that showed normal development of SEs. Altogether, our results open new perspectives in the optimization of culture conditions for A. angustifolia somatic embryogenesis, as well as establishing biochemical markers for the early selection of ECs during maturation trials.
Asunto(s)
Etilenos/análisis , Reguladores del Crecimiento de las Plantas/análisis , Poliaminas/análisis , Proteómica , Especies Reactivas de Oxígeno/análisis , Tracheophyta/metabolismo , Biomarcadores , Brasil , Electroforesis en Gel Bidimensional , Proteínas de Plantas/aislamiento & purificación , Proteínas de Plantas/metabolismo , Técnicas de Embriogénesis Somática de Plantas , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Tracheophyta/químicaRESUMEN
Araucaria angustifolia is an endangered Brazilian native conifer tree. The aim of the present work was to identify differentially expressed proteins between mature and germinated embryos of A. angustifolia, using one and two dimensional gel electrophoresis approaches followed by protein identification by tandem mass spectrometry. The identities of 32 differentially expressed protein spots from two dimensional gel maps were successfully determined, including proteins and enzymes involved in storage mobilization such as the vicilin-like storage protein and proteases. A label free approach, based on spectral counts, resulted in detection of 10 and 14 mature and germinated enriched proteins, respectively. Identified proteins were mainly related to energetic metabolism pathways, translational processes, oxidative stress regulation and cellular signaling. The integrated use of both strategies permitted a comprehensive protein expression overview of changes in germinated embryos in relation to matures, providing insights into the this process in a recalcitrant seed species. Applications of the data generated on the monitoring and control of in vitro somatic embryos were discussed.