Transcriptional repression in stochastic gene expression, patterning, and cell fate specification

Development is often driven by signaling and lineage-specific cues, yielding highly uniform and reproducible outcomes. Development also involves mechanisms that generate noise in gene expression and random patterns across tissues. Cells sometimes randomly choose between two or more cell fates in a mechanism called stochastic cell fate specification. This process diversifies cell types in otherwise homogenous tissues. Stochastic mechanisms have been extensively studied in prokaryotes where noisy gene activation plays a pivotal role in controlling cell fates. In eukaryotes, transcriptional repression stochastically limits gene expression to generate random patterns and specify cell fates. Here, we review our current understanding of repressive mechanisms that produce random patterns of gene expression and cell fates in flies, plants, mice, and humans.

From Plant Survival Under Severe Stress to Anti-Viral Human Defense - A Perspective That Calls for Common Efforts

Reprogramming of primary virus-infected cells is the critical step that turns viral attacks harmful to humans by initiating super-spreading at cell, organism and population levels. To develop early anti-viral therapies and proactive administration, it is important to understand the very first steps of this process. Plant somatic embryogenesis (SE) is the earliest and most studied model for de novo programming upon severe stress that, in contrast to virus attacks, promotes individual cell and organism survival. We argued that transcript level profiles of target genes established from in vitro SE induction as reference compared to virus-induced profiles can identify differential virus traits that link to harmful reprogramming. To validate this hypothesis, we selected a standard set of genes named 'ReprogVirus'. This approach was recently applied and published. It resulted in identifying 'CoV-MAC-TED', a complex trait that is promising to support combating SARS-CoV-2-induced cell reprogramming in primary infected nose and mouth cells. In this perspective, we aim to explain the rationale of our scientific approach. We are highlighting relevant background knowledge on SE, emphasize the role of alternative oxidase in plant reprogramming and resilience as a learning tool for designing human virus-defense strategies and, present the list of selected genes. As an outlook, we announce wider data collection in a 'ReprogVirus Platform' to support anti-viral strategy design through common efforts.

cROStalk for Life: Uncovering ROS Signaling in Plants and Animal Systems, from Gametogenesis to Early Embryonic Development

This review explores the role of reactive oxygen species (ROS)/Ca2+ in communication within reproductive structures in plants and animals. Many concepts have been described during the last years regarding how biosynthesis, generation products, antioxidant systems, and signal transduction involve ROS signaling, as well as its possible link with developmental processes and response to biotic and abiotic stresses. In this review, we first addressed classic key concepts in ROS and Ca2+ signaling in plants, both at the subcellular, cellular, and organ level. In the plant science field, during the last decades, new techniques have facilitated the in vivo monitoring of ROS signaling cascades. We will describe these powerful techniques in plants and compare them to those existing in animals. Development of new analytical techniques will facilitate the understanding of ROS signaling and their signal transduction pathways in plants and mammals. Many among those signaling pathways already have been studied in animals; therefore, a specific effort should be made to integrate this knowledge into plant biology. We here discuss examples of how changes in the ROS and Ca2+ signaling pathways can affect differentiation processes in plants, focusing specifically on reproductive processes where the ROS and Ca2+ signaling pathways influence the gametophyte functioning, sexual reproduction, and embryo formation in plants and animals. The study field regarding the role of ROS and Ca2+ in signal transduction is evolving continuously, which is why we reviewed the recent literature and propose here the potential targets affecting ROS in reproductive processes. We discuss the opportunities to integrate comparative developmental studies and experimental approaches into studies on the role of ROS/ Ca2+ in both plant and animal developmental biology studies, to further elucidate these crucial signaling pathways.

ROS and Ions in Cell Signaling during Sexual Plant Reproduction

Pollen grain is a unique haploid organism characterized by two key physiological processes: activation of metabolism upon exiting dormancy and polar tube growth. In gymnosperms and flowering plants, these processes occur in different time frames and exhibit important features; identification of similarities and differences is still in the active phase. In angiosperms, the growth of male gametophyte is directed and controlled by its microenvironment, while in gymnosperms it is relatively autonomous. Recent reviews have detailed aspects of interaction between angiosperm female tissues and pollen such as interactions between peptides and their receptors; however, accumulated evidence suggests low-molecular communication, in particular, through ion exchange and ROS production, equally important for polar growth as well as for pollen germination. Recently, it became clear that ROS and ionic currents form a single regulatory module, since ROS production and the activity of ion transport systems are closely interrelated and form a feedback loop.

Plant Cell and Organism Development

Plants represent a unique and fascinating group of living organisms [...].

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.

The mechanism and function of active DNA demethylation in plants

DNA methylation is a conserved and important epigenetic mark in both mammals and plants. DNA methylation can be dynamically established, maintained, and removed through different pathways. In plants, active DNA demethylation is initiated by the RELEASE OF SILENCING 1 (ROS1) family of bifunctional DNA glycosylases/lyases. Accumulating evidence suggests that DNA demethylation is important in many processes in plants. In this review, we summarize recent studies on the enzymes and regulatory factors that have been identified in the DNA demethylation pathway. We also review the functions of active DNA demethylation in plant development as well as biotic and abiotic stress responses. Finally, we highlight those aspects of DNA demethylation that require additional research.

The Dead Can Nurture: Novel Insights into the Function of Dead Organs Enclosing Embryos

Plants have evolved a variety of dispersal units whereby the embryo is enclosed by various dead protective layers derived from maternal organs of the reproductive system including seed coats (integuments), pericarps (ovary wall, e.g., indehiscent dry fruits) as well as floral bracts (e.g., glumes) in grasses. Commonly, dead organs enclosing embryos (DOEEs) are assumed to provide a physical shield for embryo protection and means for dispersal in the ecosystem. In this review article, we highlight recent studies showing that DOEEs of various species across families also have the capability for long-term storage of various substances including active proteins (hydrolases and ROS detoxifying enzymes), nutrients and metabolites that have the potential to support the embryo during storage in the soil and assist in germination and seedling establishment. We discuss a possible role for DOEEs as natural coatings capable of "engineering" the seed microenvironment for the benefit of the embryo, the seedling and the growing plant.

The suspensor as a model system to study the mechanism of cell fate specification during early embryogenesis

The advances in the suspensor. During early embryogenesis, the proembryo consists of two domains, the embryo proper and the suspensor. Unlike the embryo proper, which has been investigated extensively, research on the suspensor has been limited in past decades. Recent studies have revealed that the suspensor plays an important role in early embryogenesis and the process of suspensor formation and degeneration may provide a unique model for studies on cell division pattern, cell fate determination, and cell death. In this review, we briefly summarize the advances in research on the suspensor, which provide new insight in our understanding of the mechanism of early embryogenesis and show great potential for a unique model for future investigations.

Functions of IQD proteins as hubs in cellular calcium and auxin signaling: A toolbox for shape formation and tissue-specification in plants?

Calcium (Ca²⁺) ions play pivotal roles as second messengers in intracellular signal transduction, and coordinate many biological processes. Changes in intracellular Ca²⁺ levels are perceived by Ca²⁺ sensors such as calmodulin (CaM) and CaM-like (CML) proteins, which transduce Ca²⁺ signals into cellular responses by regulation of diverse target proteins. Insights into molecular functions of CaM targets are thus essential to understand the molecular and cellular basis of Ca²⁺ signaling. During the last decade, IQ67-domain (IQD) proteins emerged as the largest class of CaM targets in plants with mostly unknown functions. In the March issue of Plant Physiology, we presented the first comprehensive characterization of the 33-membered IQD family in Arabidopsis thaliana. We showed, by analysis of the subcellular localization of translational green fluorescent protein (GFP) fusion proteins, that most IQD members label microtubules (MTs), and additionally often localize to the cell nucleus or to membranes, where they recruit CaM Ca²⁺ sensors. Important functions at MTs are supported by altered MT organization and plant growth in IQD gain-of-function lines. Because IQD proteins share structural hallmarks of scaffold proteins, we propose roles of IQDs in the assembly of macromolecular complexes to orchestrate Ca²⁺ CaM signaling from membranes to the nucleus. Interestingly, expression of several IQDs is regulated by auxin, which suggests functions of IQDs as hubs in cellular auxin and calcium signaling to regulate plant growth and development.

Early plant embryogenesis-dark ages or dark matter?

In nearly all flowering plants, the basic body plan is laid down during embryogenesis. In Arabidopsis, the crucial cell types are established extremely early as reflected in the stereotypic sequence of oriented cell divisions in the developing young embryo. Research into early embryogenesis was especially focused on the role of the infamous tryptophan derivative auxin in establishing embryo polarity and generating the main body axis. However, it is becoming obvious that the mere link to auxin does not provide any mechanistic understanding of early embryo patterning. Taking recent research into account, we discuss mechanisms underlying early embryonic patterning from an evolutionary perspective.

Species Diversity Distribution Patterns of Chinese Endemic Seed Plants Based on Geographical Regions

Based on a great number of literatures, we established the database about the Chinese endemic seed plants and analyzed the compositions, growth form, distribution and angiosperm original families of them within three big natural areas and seven natural regions. The results indicate that the above characters of Chinese endemic plants take on relative rule at the different geographical scales. Among the three big natural areas, Eastern Monsoon area has the highest endemic plants richness, whereas Northwest Dryness area is the lowest. For life forms, herbs dominate. In contrast, the proportion of herbs of Eastern Monsoon area is remarkable under other two areas. Correspondingly the proportions of trees and shrubs are substantially higher than other two. For angiosperm original families, the number is the highest in Eastern Monsoon area, and lowest in Northwest Dryness area. On the other hand, among the seven natural regions, the humid and subtropical zone in Central and Southern China has the highest endemic plants richness, whereas the humid, hemi-humid region and temperate zone in Northeast China has the lowest. For life forms, the proportion of herbs tends to decrease from humid, hemi-humid region and temperate zone in Northeast China to humid and tropical zone in Southern China. Comparably, trees, shrubs and vines or lianas increase with the same directions. This fully represents these characters of Chinese endemic plants vary with latitudinal gradients. Furthermore, as to the number of endemic plants belonging to angiosperm original families, the number is the most in humid and subtropical zone in Center and Southern China, and tropical zone in Southern China in the next place. In contrast, the endemic plant of these two regions relatively is richer than that of The Qinghai-Tibet alpine and cold region. All above results sufficiently reflect that the Chinese endemic plants mainly distribute in Eastern Monsoon area, especially humid and subtropical zone in Center and Southern China and tropical zone in Southern China. Furthermore, the flora of Eastern Monsoon area, in particular humid and subtropical zone in Center and Southern China and tropical zone in Southern China, is more ancient and original than that of Northwest Dryness area and Qinghai-Tibet alpine and cold area.

Regulatory function of homeodomain-leucine zipper (HD-ZIP) family proteins during embryogenesis

Homeodomain-leucine zipper proteins (HD-ZIPs) form a plant-specific family of transcription factors functioning as homo- or heterodimers. Certain members of all four classes of this family are involved in embryogenesis, the focus of this review. They support auxin biosynthesis, transport and response, which are in turn essential for the apical-basal patterning of the embryo, radicle formation and outgrowth of the cotyledons. They transcriptionally regulate meristem regulators to maintain the shoot apical meristem once it is initiated. Some members are specific to the protoderm, the outermost layer of the embryo, and play a role in shoot apical meristem function. Within classes, homeodomain-leucine zippers tend to act redundantly during embryo development, and there are many examples of regulation within and between classes of homeodomain-leucine zippers. This indicates a complex network of regulation that awaits future experiments to uncover.

Introduction to provocative questions in left-right asymmetry

Left-right asymmetry is a phenomenon that has a broad appeal-to anatomists, developmental biologists and evolutionary biologists-because it is a morphological feature of organisms that spans scales of size and levels of organization, from unicellular protists, to vertebrate organs, to social behaviour. Here, we highlight a number of important aspects of asymmetry that encompass several areas of biology-cell-level, physiological, genetic, anatomical and evolutionary components-and that are based on research conducted in diverse model systems, ranging from single cells to invertebrates to human developmental disorders. Together, the contributions in this issue reveal a heretofore-unsuspected variety in asymmetry mechanisms, including ancient chirality elements that could underlie a much more universal basis to asymmetry development, and provide much fodder for thought with far reaching implications in biomedical, developmental, evolutionary and synthetic biology. The new emerging theme of binary cell-fate choice, promoted by asymmetric cell division of a deterministic cell, has focused on investigating asymmetry mechanisms functioning at the single cell level. These include cytoskeleton and DNA chain asymmetry-mechanisms that are amplified and coordinated with those employed for the determination of the anterior-posterior and dorsal-ventral axes of the embryo.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

Signaling, transcriptional regulation, and asynchronous pattern formation governing plant xylem development

In plants, vascular stem cells continue to give rise to all xylem and phloem cells, which constitute the plant vascular system. During plant vascular development, the peptide, tracheary element differentiation inhibitory factor (TDIF), regulates vascular stem cell fate in a non-cell-autonomous fashion. TDIF promotes vascular stem cell proliferation through up-regulating the transcription factor gene WUS-related HOMEOBOX4, and it suppresses xylem differentiation from vascular stem cells through the activation of Glycogen Synthase Kinase 3 proteins. VASCULAR-RELATED NAC-DOMAIN6 and 7 (VND6 and 7) are master transcription factors, and ectopic expression of VND6 and VND7 in various plants induces differentiation of different types of cells into metaxylem and protoxylem tracheary elements, respectively. These genes up-regulate genes involved in both patterned secondary cell wall formation and programmed cell death to form tracheary elements. Secondary wall patterns are formed by localized deposition of cellulose microfibrils, which is guided by cortical microtubules. Local activation of the small G-protein, Rho-type 11 determines distribution of cortical microtubules.

Zygotic genome activation and imprinting: parent-of-origin gene regulation in plant embryogenesis

Parent-of-origin dependent gene expression refers to differential activity of alleles inherited from the egg and sperm. In plants, zygotic genome activation (ZGA) and gene imprinting are two examples of this phenomenon, both of which occur during seed development. As its name implies, ZGA is a genome-wide process that occurs in embryos during the first few days after fertilization. Evidence exists that maternal alleles initially predominate during ZGA, although most genes also show some paternal activity. By contrast, imprinting can be defined as a bias in gene expression that lasts beyond the first few days of seed development. Hundreds of imprinted genes have been discovered in the endosperm, and a few have been described in the embryo. This review discusses recent advances in our understanding of the phenomena and mechanisms of ZGA and imprinting in seeds, with an emphasis on embryo development. Important unanswered questions and areas for future research are highlighted.

The Maternal-to-Zygotic Transition in Flowering Plants: Evidence, Mechanisms, and Plasticity

The maternal-to-zygotic transition (MZT) defines a developmental phase during which the embryo progressively emancipates itself from a developmental control relying largely on maternal information. The MZT is a functional readout of two processes: the clearance of maternally derived information and the de novo expression of the inherited, parental alleles enabled by zygotic genome activation (ZGA). In plants, for many years the debate about whether the MZT exists at all focused on the ZGA alone. However, several recent studies provide evidence for a progressive alleviation of the maternal control over embryogenesis that is correlated with a gradual ZGA, a process that is itself maternally controlled. Yet, several examples of zygotic genes that are expressed and/or functionally required early in embryogenesis demonstrate a certain flexibility in the dynamics and kinetics of the MZT among plant species and also intraspecific hybrids.

Seed evolution: parental conflicts in a multi-generational household

Seeds are multi-generational structures containing a small embryonic plant enclosed in layers of diverse parental origins. The evolution of seeds was a pinnacle in an evolutionary trend towards a progressive retention of embryos and gametes within parental tissue. This strategy, which dates back to the first land plants, allowed an increased protection and nourishing of the developing embryo. Flowering plants took parental control one step further with the evolution of a biparental endosperm that derives from a second parallel fertilization event. The endosperm directly nourishes the developing embryo and allows not only the maternal genes, but also paternal genes, to play an active role during seed development. The appearance of an endosperm set the conditions for the manifestation of conflicts of interest between maternal and paternal genomes over the allocation of resources to the developing embryos. As a consequence, a dynamic balance was established between maternal and paternal gene dosage in the endosperm, and maintaining a correct balance became essential to ensure a correct seed development. This balance was achieved in part by changes in the genetic constitution of the endosperm and through epigenetic mechanisms that allow a differential expression of alleles depending on their parental origin. This review discusses the evolutionary steps that resulted in the appearance of seeds and endosperm, and the epigenetic and genetic mechanisms that allow a harmonious coinhabitance of multiple generations within a single seed.

An allometric model for mapping seed development in plants

Despite a tremendous effort to map quantitative trait loci (QTLs) responsible for agriculturally and biologically important traits in plants, our understanding of how a QTL governs the developmental process of plant seeds remains elusive. In this article, we address this issue by describing a model for functional mapping of seed development through the incorporation of the relationship between vegetative and reproductive growth. The time difference of reproductive from vegetative growth is described by Reeve and Huxley’s allometric equation. Thus, the implementation of this equation into the framework of functional mapping allows dynamic QTLs for seed development to be identified more precisely. By estimating and testing mathematical parameters that define Reeve and Huxley’s allometric equations of seed growth, the dynamic pattern of the genetic effects of the QTLs identified can be analyzed. We used the model to analyze a soybean data, leading to the detection of QTLs that control the growth of seed dry weight. Three dynamic QTLs, located in two different linkage groups, were detected to affect growth curves of seed dry weight. The QTLs detected may be used to improve seed yield with marker-assisted selection by altering the pattern of seed development in a hope to achieve a maximum size of seeds at a harvest time.

Epigenetic mechanisms of postzygotic reproductive isolation in plants

Hybrid incompatibility is generally viewed as a consequence of negative epistatic interactions between alleles that do not cause negative fitness effects in their parents. Substantial evidence in support of the model has accumulated over recent years. Nevertheless, there is evidence that hybrid incompatibility can have an epigenetic basis and results from deregulated small RNAs (sRNAs), causing changes in DNA methylation and transposable element (TE) activation. Epigenetically regulated loci can impact on the expression of nearby located genes. Alteration of dosage-sensitive gene expression builds hybridization barriers in the endosperm; however, it may also offer an explanation for transgressive effects in plant hybrids. In this review we highlight recent advances that illuminate the role of epigenetic pathways in establishing hybrid incompatibility in plants.

[The role of genetic control and self-assembly in gametophyte sporoderm ontogeny: hypotheses and experiment]

A review of our own and literature data on mechanisms of sporoderm development (of the wall of pollen grains and spores) is represented here in the light of colloidal relationships-so-called micellar hypothesis (Gabarayeva and Hemsley, 2006; Hemsley and Gabarayeva, 2007) which suggests the participation of self-assembly in development. The development of the exines (ofsporopollenin-containing part of the sporo- derm) in 5 species from remote taxa has been traced in detail and interpreted as a micellar sequence. The experimental modelling of exine-like structures, carried out in vitro where physico-chemical regularities of colloidal systems (hydrophobic relationships) were the driving motive, is a strong evidence of the relevance of the micellar hypothesis and emphasizes a promising character of these studies. The correlation between ge- nomic control and self-assembly in arrangement of complex biological walls is discussed.

Initiation of vascular development

The initiation of vascular development occurs during embryogenesis and the development of lateral organs, such as lateral roots and leaves. Understanding the mechanism underlying the initiation of vascular development has been an important goal of plant biologists. Auxin flow is a crucial factor involved in the initiation of vascular development. In addition, recent studies have identified key factors that regulate the establishment of vascular initial cells in embryos and roots. In this review, we summarize the recent findings in this field and discuss the initiation of vascular development.

Somatic embryogenesis: life and death processes during apical-basal patterning

Somatic embryogenesis (SE) is a process of differentiation of cells into a plant bypassing the fusion of gametes. As such, it represents a very powerful tool in biotechnology for propagation of species with a long reproductive cycle or low seed set and production of genetically modified plants with improved traits. SE is also a versatile model to study cellular and molecular mechanisms of plant embryo patterning. The morphology and molecular regulation of SE resemble those of zygotic embryogenesis and begin with establishment of apical-basal asymmetry. The apical domain, the embryo proper, proliferates and eventually gives rise to the plantlet, while the basal part, the embryo suspensor, is terminally differentiated and gradually removed via vacuolar programmed cell death (PCD). This PCD is essential for normal development of the apical domain. Emerging evidence demonstrates that signalling events in the apical and basal domains share homologous components. Here we provide an overview of the main pathways controlling the life and death events during SE.

Gibberellic acid in plant: still a mystery unresolved

Gibberellic acid (GA), a plant hormone stimulating plant growth and development, is a tetracyclic di-terpenoid compound. GAs stimulate seed germination, trigger transitions from meristem to shoot growth, juvenile to adult leaf stage, vegetative to flowering, determines sex expression and grain development along with an interaction of different environmental factors viz., light, temperature and water. The major site of bioactive GA is stamens that influence male flower production and pedicel growth. However, this opens up the question of how female flowers regulate growth and development, since regulatory mechanisms/organs other than those in male flowers are mandatory. Although GAs are thought to act occasionally like paracrine signals do, it is still a mystery to understand the GA biosynthesis and its movement. It has not yet confirmed the appropriate site of bioactive GA in plants or which tissues targeted by bioactive GAs to initiate their action. Presently, it is a great challenge for scientific community to understand the appropriate mechanism of GA movement in plant's growth, floral development, sex expression, grain development and seed germination. The appropriate elucidation of GA transport mechanism is essential for the survival of plant species and successful crop production.