Pattern formation in the Arabidopsis embryo: a genetic perspective

Mediator complex: an important regulator of root system architecture

Mediator, a multiprotein complex, is an important component of the transcription machinery. In plants, the latest studies have established that it functions as a signal processor that conveys transcriptional signals from transcription factors to RNA polymerase II. Mediator has been found to be involved in different developmental and stress-adaptation conditions, ranging from embryo, root, and shoot development to flowering and senescence, and also in responses to different biotic and abiotic stresses. In the last decade, significant progress has been made in understanding the role of Mediator subunits in root development. They have been shown to transcriptionally regulate development of almost all the components of the root system architecture-primary root, lateral roots, and root hairs. They also have a role in nutrient acquisition by the root. In this review, we discuss all the known functions of Mediator subunits during root development. We also highlight the role of Mediator as a nodal point for processing different hormone signals that regulate root morphogenesis and growth.

Plant developmental oddities

MAIN CONCLUSION

Plants lacking shoot apical meristem develop with unique body shapes, suggesting rewiring of developmental genes. This loss of the meristem is likely influenced by a combination of environmental factors and evolutionary pressures. This study explores the development of plant bodies in three families (Podostemaceae, Lemnaceae, and Gesneriaceae) where the shoot apical meristem (SAM), a key structure for growth, is absent or altered. The review highlights alternative developmental strategies these plants employ. Also, we considered alternative reproduction in those species, namely through structures like turions, fronds, or modified leaves, bypassing the need for a SAM. Further, we report on studies based on the expression patterns of genes known to be involved in SAM formation and function. Interestingly, these genes are still present but expressed in atypical locations, suggesting a rewiring of developmental networks. Our view on the current literature and knowledge indicates that the loss or reduction of the SAM is driven by a combination of environmental pressures and evolutionary constraints, leading to these unique morphologies. Further research, also building on Next-Generation Sequencing, will be instrumental to explore the genetic basis for these adaptations and how environmental factors influence them.

Evaluating the Response of Glycine soja Accessions to Fungal Pathogen Macrophomina phaseolina during Seedling Growth

Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot.

Zygotic Embryogenesis in Flowering Plants

In the context of plant regeneration, in vitro systems to produce embryos are frequently used. In many of these protocols, nonzygotic embryos are initiated that will produce shoot-like structures but may lack a primary root. By increasing the auxin-to-cytokinin ratio in the growth medium, roots are then regenerated in a second step. Therefore, in vitro systems might not or only partially execute a similar developmental program as employed during zygotic embryogenesis. There are, however, in vitro systems that can remarkably mimic zygotic embryogenesis such as Brassica microspore-derived embryos. In this case, the patterning process of these haploid embryos closely follows zygotic embryogenesis and all fundamental tissue types are generated in a rather similar manner. In this review, we discuss the most fundamental molecular events during early zygotic embryogenesis and hope that this brief summary can serve as a reference for studying and developing in vitro embryogenesis systems in the context of doubled haploid production.

Convergent occurrence of the developmental hourglass in plant and animal embryogenesis?

BACKGROUND

The remarkable similarity of animal embryos at particular stages of development led to the proposal of a developmental hourglass. In this model, early events in development are less conserved across species but lead to a highly conserved 'phylotypic period'. Beyond this stage, the model suggests that development once again becomes less conserved, leading to the diversity of forms. Recent comparative studies of gene expression in animal groups have provided strong support for the hourglass model. How and why might such an hourglass pattern be generated? More importantly, how might early acting events in development evolve while still maintaining a later conserved stage?

SCOPE

The discovery that an hourglass pattern may also exist in the embryogenesis of plants provides comparative data that may help us explain this phenomenon. Whether the developmental hourglass occurs in plants, and what this means for our understanding of embryogenesis in plants and animals is discussed. Models by which conserved early-acting genes might change their functional role in the evolution of gene networks, how networks buffer these changes, and how that might constrain, or confer diversity, of the body plan are also discused.

CONCLUSIONS

Evidence of a morphological and molecular hourglass in plant and animal embryogenesis suggests convergent evolution. This convergence is likely due to developmental constraints imposed upon embryogenesis by the need to produce a viable embryo with an established body plan, controlled by the architecture of the underlying gene regulatory networks. As the body plan is largely laid down during the middle phases of embryo development in plants and animals, then it is perhaps not surprising this stage represents the narrow waist of the hourglass where the gene regulatory networks are the oldest and most robust and integrated, limiting species diversity and constraining morphological space.

Developmentally regulated HEART STOPPER, a mitochondrially targeted L18 ribosomal protein gene, is required for cell division, differentiation, and seed development in Arabidopsis

Evidence is presented for the role of a mitochondrial ribosomal (mitoribosomal) L18 protein in cell division, differentiation, and seed development after the characterization of a recessive mutant, heart stopper (hes). The hes mutant produced uncellularized endosperm and embryos arrested at the late globular stage. The mutant embryos differentiated partially on rescue medium with some forming callus. HES (At1g08845) encodes a mitochondrially targeted member of a highly diverged L18 ribosomal protein family. The substitution of a conserved amino residue in the hes mutant potentially perturbs mitoribosomal function via altered binding of 5S rRNA and/or influences the stability of the 50S ribosomal subunit, affecting mRNA binding and translation. Consistent with this, marker genes for mitochondrial dysfunction were up-regulated in the mutant. The slow growth of the endosperm and embryo indicates a defect in cell cycle progression, which is evidenced by the down-regulation of cell cycle genes. The down-regulation of other genes such as EMBRYO DEFECTIVE genes links the mitochondria to the regulation of many aspects of seed development. HES expression is developmentally regulated, being preferentially expressed in tissues with active cell division and differentiation, including developing embryos and the root tips. The divergence of the L18 family, the tissue type restricted expression of HES, and the failure of other L18 members to complement the hes phenotype suggest that the L18 proteins are involved in modulating development. This is likely via heterogeneous mitoribosomes containing different L18 members, which may result in differential mitochondrial functions in response to different physiological situations during development.

Core pathways controlling shoot meristem maintenance

Essential to the function of shoot meristems in plants to act as sites of continuous organ and tissue formation is the ability of cells within the meristem to remain undifferentiated and proliferate indefinitely. These are characteristics of the stem cells within meristems that are critical for their growth properties. Stem cells are found in tight association with the stem cell niche-those cells that signal to maintain stem cells. Shoot meristems are unique among stem cell systems in that the stem cell niche is a constantly changing population of recent daughter stem cells. Recent progress from Arabidopsis and other systems have uncovered a large number of genes with defined roles in meristem structure and maintenance. This review will focus on well-studied pathways that represent signaling between the stem cells and the niche, that prevent ectopic differentiation of stem cells, that regulate the chromatin status of stem cell factors, and that reveal intersection of hormone signaling and meristem maintenance.

In silico analyses of pericycle cell populations reinforce their relation with associated vasculature in Arabidopsis

In Arabidopsis, lateral root initiation occurs in a subset of pericycle cells at the xylem pole that will divide asymmetrically to give rise to a new lateral root organ. While lateral roots never develop at the phloem pole, it is unclear how the interaction with xylem and phloem poles determines the distinct pericycle identities with different competences. Nevertheless, pericycle cells at these poles are marked by differences in size, by ultrastructural features and by specific proteins and gene expression. Here, we provide transcriptional evidence that pericycle cells are intimately associated with their vascular tissue instead of being a separate concentric layer. This has implications for the identification of cell- and tissue-specific promoters that are necessary to drive and/or alter gene expression locally, avoiding pleiotropic effects. We were able to identify a small set of genes that display specific expression in the phloem or xylem pole pericycle cells, and we were able to identify motifs that are likely to drive expression in either one of those tissues.

Mechanistic framework for establishment, maintenance, and alteration of cell polarity in plants

Cell polarity establishment, maintenance, and alteration are central to the developmental and response programs of nearly all organisms and are often implicated in abnormalities ranging from patterning defects to cancer. By residing at the distinct plasma membrane domains polar cargoes mark the identities of those domains, and execute localized functions. Polar cargoes are recruited to the specialized membrane domains by directional secretion and/or directional endocytic recycling. In plants, auxin efflux carrier PIN proteins display polar localizations in various cell types and play major roles in directional cell-to-cell transport of signaling molecule auxin that is vital for plant patterning and response programs. Recent advanced microscopy studies applied to single cells in intact plants reveal subcellular PIN dynamics. They uncover the PIN polarity generation mechanism and identified important roles of AGC kinases for polar PIN localization. AGC kinase family members PINOID, WAG1, and WAG2, belonging to the AGC-3 subclass predominantly influence the polar localization of PINs. The emerging mechanism for AGC-3 kinases action suggests that kinases phosphorylate PINs mainly at the plasma membrane after initial symmetric PIN secretion for eventual PIN internalization and PIN sorting into distinct ARF-GEF-regulated polar recycling pathways. Thus phosphorylation status directs PIN translocation to different cell sides. Based on these findings a mechanistic framework evolves that suggests existence of cell side-specific recycling pathways in plants and implicates AGC3 kinases for differential PIN recruitment among them for eventual PIN polarity establishment, maintenance, and alteration.

NOF1 encodes an Arabidopsis protein involved in the control of rRNA expression

The control of ribosomal RNA biogenesis is essential for the regulation of protein synthesis in eukaryotic cells. Here, we report the characterization of NOF1 that encodes a putative nucleolar protein involved in the control of rRNA expression in Arabidopsis. The gene has been isolated by T-DNA tagging and its function verified by the characterization of a second allele and genetic complementation of the mutants. The nof1 mutants are affected in female gametogenesis and embryo development. This result is consistent with the detection of NOF1 mRNA in all tissues throughout plant life's cycle, and preferentially in differentiating cells. Interestingly, the closely related proteins from zebra fish and yeast are also necessary for cell division and differentiation. We showed that the nof1-1 mutant displays higher rRNA expression and hypomethylation of rRNA promoter. Taken together, the results presented here demonstrated that NOF1 is an Arabidopsis gene involved in the control of rRNA expression, and suggested that it encodes a putative nucleolar protein, the function of which may be conserved in eukaryotes.

Mechanisms of Pattern Formation in Plant Embryogenesis

Many of the patterning mechanisms in plants were discovered while studying postembryonic processes and resemble mechanisms operating during animal development. The emergent role of the plant hormone auxin, however, seems to represent a plant-specific solution to multicellular patterning. This review summarizes our knowledge on how diverse mechanisms that were first dissected at the postembryonic level are now beginning to provide an understanding of plant embryogenesis.

AtNAP7 is a plastidic SufC-like ATP-binding cassette/ATPase essential for Arabidopsis embryogenesis

In bacteria, yeast, and mammals, iron-sulfur (Fe-S) cluster-containing proteins are involved in numerous processes including electron transfer, metabolic reactions, sensing, signaling, and regulation of gene expression. In humans, iron-storage diseases such as X-linked sideroblastic anemia and ataxia are caused by defects in Fe-S cluster availability. The biogenesis of Fe-S clusters involves several pathways, and in bacteria, the SufABCDSE operon has been shown to play a vital role in Fe-S biogenesis and repair during oxidative stress. Although Fe-S proteins play vital roles in plants, Fe-S cluster biogenesis and maintenance and physiological consequences of dysfunctional Fe-S cluster assembly remains obscure. Here we report that Arabidopsis plants deficient for the SufC homolog AtNAP7 show lethality at the globular stage of embryogenesis. AtNAP7 is expressed in developing embryos and in apical, root, and floral meristems and encodes an ATP-binding cassette/ATPase that can partially rescue growth defects in an Escherichia coli SufC mutant during oxidative stress. AtNAP7 is plastid-localized, and mutant embryos contain abnormal developing plastids with disorganized thylakoid structures. We found that AtNAP7 can interact with AtNAP6, a plastidic Arabidopsis SufD homolog, and because Arabidopsis plastids also harbor SufA, SufB, SufS, and SufE homologs, plastids probably contain a complete SUF system. Our results imply that AtNAP7 represents a conserved SufC protein involved in the biogenesis and/or repair of oxidatively damaged Fe-S clusters and suggest an important role for plastidic Fe-S cluster maintenance and repair during Arabidopsis embryogenesis.

The pleiotropic mutation dar1 affects plant architecture in Arabidopsis thaliana

Shoot architecture is shaped upon the organogenic activity of the shoot apical meristem (SAM). Such an activity relies on the balance between the maintenance of a population of undifferentiated cells in the centre of the SAM and the recruitment of organ founder cells at the periphery. A novel mutation in Arabidopsis thaliana, distorted architecture1 (dar1), is characterised by disturbed phyllotaxy of the inflorescence and consumption of the apical meristem late in development. SEM and light microscopy analyses of the dar1 SAM reveal an abnormal partitioning of meristematic domains, and mutations known to affect the SAM structure and function were found to interact with dar1. Moreover, the mutant shows an alteration of the root apical meristem (RAM) structure. Those observations support the hypothesis that DAR1 has a role in meristem maintenance and it is required for the normal development of Arabidopsis inflorescence during plant life.

RASPBERRY3 gene encodes a novel protein important for embryo development

We identified a new gene that is interrupted by T-DNA in an Arabidopsis embryo mutant called raspberry3. raspberry3 has "raspberry-like" cellular protuberances with an enlarged suspensor characteristic of other raspberry embryo mutants, and is arrested morphologically at the globular stage of embryo development. The predicted RASPBERRY3 protein has domains found in proteins present in prokaryotes and algae chloroplasts. Computer prediction analysis suggests that the RASPBERRY3protein may be localized in the chloroplast. Complementation analysis supports the possibility that the RASPBERRY3 protein may be involved in chloroplast development. Our experiments demonstrate the important role of the chloroplast, directly or indirectly, in embryo morphogenesis and development.

Genetic and epigenetic processes in seed development

Seed development has emerged as an important area of research in plant development. Recent research has highlighted the divergent reproductive strategies of the male and female genomes and interaction between genetic and epigenetic control mechanisms. Isolation of genes involved in embryo and endosperm development is leading to an understanding of the regulation of these processes at the molecular level. A thorough grasp of these processes will not only illuminate an important area of plant development but will also have an impact on agronomy by helping to facilitate food production. An understanding of seed development is also likely to clarify the molecular mechanisms of apomixis, a fascinating process of asexual seed production present in many plants.