Picky eaters: selective autophagy in plant cells Cadena‐Ramos, Alexis I.; De‐la‐Peña, Clelia
The Plant journal : for cell and molecular biology,
January 2024, 2024-Jan, 2024-01-00, 20240101, Letnik:
117, Številka:
2
Journal Article
Recenzirano
SUMMARY
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been ...extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy‐related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
Significance Statement
This review unravels the intricate interplay between selective autophagy and regulatory mechanisms in plant cells, providing valuable insights into crucial processes. Understanding these interactions expands our comprehension of cellular adaptation, nutrient responses, and holds promise for targeted interventions in plant physiology with implications across various scientific domains.
Albino plants display partial or complete loss of photosynthetic pigments and defective thylakoid membrane development, consequently impairing plastid function and development. These distinctive ...attributes render albino plants excellent models for investigating chloroplast biogenesis. Despite their potential, limited exploration has been conducted regarding the molecular alterations underlying these phenotypes, extending beyond photosynthetic metabolism. In this study, we present a novel de novo transcriptome assembly of an albino somaclonal variant of Agave angustifolia Haw., which spontaneously emerged during the micropropagation of green plantlets. Additionally, RT‐qPCR analysis was employed to validate the expression of genes associated with chloroplast biogenesis, and plastome copy numbers were quantified. This research aims to gain insight into the molecular disruptions affecting chloroplast development and ascertain whether the expression of critical genes involved in plastid development and differentiation is compromised in albino tissues of A. angustifolia. Our transcriptomic findings suggest that albino Agave plastids exhibit high proliferation, activation of the protein import machinery, altered transcription directed by PEP and NEP, dysregulation of plastome expression genes, reduced expression of photosynthesis‐associated nuclear genes, disruption in the tetrapyrrole and carotenoid biosynthesis pathway, alterations in the plastid ribosome, and an increased number of plastome copies, among other alterations.
Throughout decades of plant research, the plant hormones known as auxins have been found to be of vital importance in most plant development processes. Indole-3-acetic acid (IAA) represents the most ...common auxin in plants and can be synthesized from its tryptophan precursor, which is synthesized in the chloroplast. The chloroplast constitutes an organelle of great relevance to plants since the photosynthesis process by which plants get most of their energy is carried out there. The role of auxins in photosynthesis has been studied for at least 50 years, and in this time, it has been shown that auxins have an effect on several of the essential components and structure of the chloroplast. In recent decades, a high number of genes have been reported to be expressed in the chloroplast and some of their mutants have been shown to alter different auxin-mediated pathways. Genes in signaling pathways such as
IAA/AUX
,
ARF
,
GH.3
,
SAUR
and
TIR
, biosynthesis-related genes such as
YUCCA
and transport-related genes such as
PIN
have been identified among the most regulated genes in mutants related to alterations in the chloroplast. This review aims to provide a complete and updated summary of the relationship between auxins and several processes that involve the chloroplast, including chloroplast development, plant albinism, redox regulation and pigment synthesis.
Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The ...success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.
Display omitted
•Micropropagation culture stress provokes somaclonal variation in A. angustifolia.•Nutrient starvation for long periods promotes DNA methylation.•Cytokinin increases somaclonal ...variation emergence but intensifies shoot formation.•High concentrations of 6-benzyladenine promote elevated shoot production in albino plants.
Somaclonal variation (SV) is observed during micropropagation, especially in organogenic processes when differentiated somatic cells are induced into a pluripotent state. However, the clones obtained show differences in phenotype from each other and from the mother plants, which could be an agricultural problem or an ornamental advantage. Few of the mechanisms associated with how a somatic cell generates phenotypic variation have been elucidated. Recently, our group demonstrated that an albino phenotype produced in Agave in in vitro culture was linked to changes in DNA methylation through the micropropagation process, suggesting a new way to investigate the mechanism. Therefore, here we evaluate the effect of stressful conditions in the culture media on three different phenotypes (green, variegated and albino) of Agaveangustifolia Haw. to determine the changes in DNA methylation linked to SV in the new formed shoots. The effects of nutrient availability and exogen cytokinin concentration in the culture media were evaluated for five months in each phenotype. We observed that a reduction of 25 % in the nutrients in the culture media affected the coloration of green plantlets. On the other hand, a high 6-benzyladenine (BA) concentration exposure (88.8 μM) in the variegated phenotype enhanced organogenic capability, increased phenotypic variation, and changed DNA methylation levels. We have demonstrated that long periods of time under nutrient-limited conditions or high cytokinin concentration provoke changes in DNA methylation levels that increase SV frequency in the newly formed shoots. Epigenetic changes may thus be an overlooked factor in SV induced by culture media stress.
Somatic embryogenesis (SE) is a powerful tool for plant genetic improvement when used in combination with traditional agricultural techniques, and it is also an important technique to understand the ...different processes that occur during the development of plant embryogenesis. SE onset depends on a complex network of interactions among plant growth regulators, mainly auxins and cytokinins, during the proembryogenic early stages, and ethylene and gibberellic and abscisic acids later in the development of the somatic embryos. These growth regulators control spatial and temporal regulation of multiple genes in order to initiate change in the genetic program of somatic cells, as well as moderating the transition between embryo developmental stages. In recent years, epigenetic mechanisms have emerged as critical factors during SE. Some early reports indicate that auxins and in vitro conditions modify the levels of DNA methylation in embryogenic cells. The changes in DNA methylation patterns are associated with the regulation of several genes involved in SE, such as WUS, BBM1, LEC, and several others. In this review, we highlight the more recent discoveries in the understanding of the role of epigenetic regulation of SE. In addition, we include a survey of different approaches to the study of SE, and new opportunities to focus SE studies.
Reproduction is one of the most important phases in an organism’s lifecycle. In the case of angiosperm plants, flowering provides the major developmental transition from the vegetative to the ...reproductive stage, and requires genetic and epigenetic reprogramming to ensure the success of seed production. Flowering is regulated by a complex network of genes that integrate multiple environmental cues and endogenous signals so that flowering occurs at the right time; hormone regulation, signaling and homeostasis are very important in this process. Working alone or in combination, hormones are able to promote flowering by epigenetic regulation. Some plant hormones, such as gibberellins, jasmonic acid, abscisic acid and auxins, have important effects on chromatin compaction mediated by DNA methylation and histone posttranslational modifications, which hints at the role that epigenetic regulation may play in flowering through hormone action. miRNAs have been viewed as acting independently from DNA methylation and histone modification, ignoring their potential to interact with hormone signaling – including the signaling of auxins, gibberellins, ethylene, jasmonic acid, salicylic acid and others – to regulate flowering. Therefore, in this review we examine new findings about interactions between epigenetic mechanisms and key players in hormone signaling to coordinate flowering.
Microbes and plants have evolved biochemical mechanisms to communicate with each other. The molecules responsible for such communication are secreted during beneficial or harmful interactions. ...Hundreds of these molecules secreted into the rhizosphere have been identified, and their functions are being studied in order to understand the mechanisms of interaction and communication among the different members of the rhizosphere community. The importance of root and microbe secretion to the underground habitat in improving crop productivity is increasingly recognized, with the discovery and characterization of new secreting compounds found in the rhizosphere. Different omic approaches, such as genomics, transcriptomics, proteomics, and metabolomics, have expanded our understanding of the first signals between microbes and plants. In this review, we highlight the more recent discoveries related to molecules secreted into the rhizosphere and how they affect plant productivity, either negatively or positively. In addition, we include a survey of novel approaches to studying the rhizosphere and emerging opportunities to direct future studies.
Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able ...to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.
PDF
