Plant small RNAs as morphogens

RNA interference (RNAi) in plants has long been known to produce a non-cell autonomous signal capable of silencing target genes over great cellular distances. However, only recently have RNAi-derived small RNAs been formally shown to comprise that mobile signal. Interestingly, some of these mobile small RNAs play critical roles in plant development, forming gradients that regulate the activity of their targets in a dosage-dependent manner. These properties resemble features of morphogens in animals, leading us to postulate that such cell-fate-defining small RNAs employ similar principles for the generation, stabilization and interpretation of their expression gradients. Here we review our understanding of small RNA mobility in plants, evaluate their potential as morphogen-like signals, and consider how the graded accumulation patterns that underlie their patterning/biological activity could be created and maintained.     

Threshold-dependent BMP-mediated repression: a model for a conserved mechanism that patterns the neuroectoderm

Subdivision of the neuroectoderm into three rows of cells along the dorsal-ventral axis by neural identity genes is a highly conserved developmental process. While neural identity genes are expressed in remarkably similar patterns in vertebrates and invertebrates, previous work suggests that these patterns may be regulated by distinct upstream genetic pathways. Here we ask whether a potential conserved source of positional information provided by the BMP signaling contributes to patterning the neuroectoderm. We have addressed this question in two ways: First, we asked whether BMPs can act as bona fide morphogens to pattern the Drosophila neuroectoderm in a dose-dependent fashion, and second, we examined whether BMPs might act in a similar fashion in patterning the vertebrate neuroectoderm. In this study, we show that graded BMP signaling participates in organizing the neural axis in Drosophila by repressing expression of neural identity genes in a threshold-dependent fashion. We also provide evidence for a similar organizing activity of BMP signaling in chick neural plate explants, which may operate by the same double negative mechanism that acts earlier during neural induction. We propose that BMPs played an ancestral role in patterning the metazoan neuroectoderm by threshold-dependent repression of neural identity genes.     

Origins of the other metazoan body plans: the evolution of larval forms

Bilaterian animal body plan origins are not solely about adult forms. Most animals have larvae with body plans, ontogenies and ecologies distinct from adults. There are two primary hypotheses for larval origins. The first hypothesis suggests that the first animals were small pelagic forms similar to modern larvae, with adult bilaterian body plans evolved subsequently. The second hypothesis suggests that adult bilaterian body plans evolved first and that larval body plans arose by interpolation of features into direct-developing ontogenies. The two hypotheses have different consequences for understanding parsimony in evolution of larvae and of developmental genetic mechanisms. If primitive metazoans were like modern larvae and distinct adult forms evolved independently, there should be little commonality of patterning genes among adult body plans. However, sharing of patterning genes is observed. If larvae arose by co-option of adult bilaterian-expressed genes into independently evolved larval forms, larvae may show morphological convergence, but with distinct patterning genes, and this is observed. Thus, comparative studies of gene expression support independent origins of larval features. Precambrian and Cambrian embryonic fossils are also consistent with direct development of the adult as being primitive, with planktonic larvae arising during the Cambrian. Larvae have continued to co-opt genes and evolve new features, allowing study of developmental evolution.     

Reversed animal-plant interactions: the evolution of insectivorous and ant-fed plants

Insectivorous plants and ant-fed plants represent the two ways in which plants have evolved to utilize directly nutrients derived from animals. This paper addresses the limitations under which selection acts to favour the evolution of one or the other of these nutrient-gathering tactics. Both tactics have evolved independently at least six times under similar ecological conditions, indicating that the evolutionary solutions to ecological problems are limited by the historical make-up of communities and are, to some extent, predictable. Both insectivorous and ant-fed plants evolve in environments with very low levels of availability of nutrients in the substrate; the primary use of the animal-food is probably nitrogen; the vast majority of species are perennial, and most species are tropical or subtropical, although some insectivorous genera are primarily temperate.
Although these two nutrient-gathering tactics evolve in response to similar ecological problems, whether plants evolve an insectivorous habit or the ant-fed habit depends on the growth forms of the plants and the habitats in which they grow. Most insectivorous plants evolve as herbs in wet, sterile soils or in sterile aquatic habitats; ant-fed plants evolve as epiphytes on trees in open-canopied habitats. These kinds of animal-plant interactions are relatively rare because the environments in which they are favoured by selection are uncommon.     

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean ‘flower’ are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression.     

Morphing into cancer: the role of developmental signaling pathways in brain tumor formation

Morphogens play a critical role in most aspects of development, including expansion and patterning of the central nervous system. Activating germline mutations in components of the Hedgehog and Wnt pathways have provided evidence for the important roles morphogens play in the genesis of brain tumors such as cerebellar medulloblastoma. In addition, aberrant expression of transforming growth factor-beta (TGF-beta) superfamily members has been demonstrated to contribute to progression of malignant gliomas. This review summarizes our current knowledge about the roles of morphogens in central nervous system tumorigenesis.     

Morphogens, nutrients, and the basis of organ scaling

The regulation of organ size is a long-standing problem in animal development. Studies in this area have shown that organ-intrinsic patterning morphogens influence organ size, guiding growth in accordance with positional information. However, organ-extrinsic humoral factors such as insulin also affect organ size, synchronizing growth with nutrient levels. Proliferating cells must integrate instructions from morphogens with those from nutrition so that growth proceeds as a function of both inputs. Coordinating cell proliferation with morphogens and nutrients ensures organs scale appropriately with body size, but the basis of this coordination is unclear. Here, the problem is illustrated using the Drosophila wing--a paradigm for organ growth and size control--and a potential solution suggested.     

Dynamics of maternal morphogen gradients in Drosophila

The first direct studies of morphogen gradients were done in the end of 1980s, in the early Drosophila embryo, which is patterned under the action of four maternally determined morphogens. Since the early studies of maternal morphogens were done with fixed embryos, they were viewed as relatively static signals. Several recent studies analyze dynamics of the anterior, dorsoventral, and terminal patterning signals. The results of these quantitative studies provide critical tests of classical models and reveal new modes of morphogen regulation and readout in one of the most extensively studied patterning systems.     

Plants, animals and the logic of development

Multicellular plants and animals have evolved independently from a unicellular, last common ancestor. Each lineage started with a common toolkit of functioning genes and evolved to complex, multicellular forms. Comparison of the genes used to serve similar functions shows how organisms can use different genes for similar ends and thereby reveals the principles of development.     

Auxin transport-feedback models of patterning in plants

Many patterning events in plants are regulated by the phytohormone auxin. In fact, so many things are under the influence of auxin that it seems difficult to understand how a single hormone can do so much. Auxin moves throughout the plant via a network of specialized membrane-bound import and export proteins, which are often differentially expressed and polarized depending on tissue type. Here, we review simulation models of pattern formation that are based on the control of these transporters by auxin itself. In these transport-feedback models, diversity in patterning comes not from the addition of more morphogens, but rather by varying the mechanism that regulates the transporters.     

Plant evolution and development in a post-genomic context

Large-scale gene-sequencing projects that have been undertaken in animals have involved organisms from contrasting taxonomic groups, such as worm, fly and mammal. By contrast, similar botanical projects have focused exclusively on flowering plants. This has made it difficult to carry out fundamental research on how plants have evolved from simple to complex forms - a task that has been very successful in animals. However, in the flowering plants, the many completely or partially sequenced genomes now becoming available will provide a powerful tool to investigate the details of evolution in one group of related organisms.     

Plants, animals and the logic of development

Multicellular plants and animals have evolved independently from a unicellular, last common ancestor. Each lineage started with a common toolkit of functioning genes and evolved to complex, multicellular forms. Comparison of the genes used to serve similar functions shows how organisms can use different genes for similar ends and thereby reveals the principles of development.     

Plants, animals and the logic of development

Multicellular plants and animals have evolved independently from a unicellular, last common ancestor. Each lineage started with a common toolkit of functioning genes and evolved to complex, multicellular forms. Comparison of the genes used to serve similar functions shows how organisms can use different genes for similar ends and thereby reveals the principles of development.     

Morphogen gradients in vertebrate limb development.

The developing limb is an excellent model for pattern formation in vertebrate embryos. Signalling by the polarizing region controls limb pattern across the antero-posterior axis of the chick limb. It was suggested first on theoretical grounds that signalling by the polarizing region could involve a morphogen gradient. Embryological manipulations provided evidence consistent with this model and, more recently, signalling molecules associated with the polarizing region have been identified and tested for their role as morphogens. It is still not clear whether any of the known molecules act directly as a morphogen. The extension of the morphogen model to patterning along the other axes of the limb has been proposed but this may not be applicable.     

The interplay between morphogens and tissue growth

Morphogens are conserved, secreted signalling molecules that regulate the size, shape and patterning of animal tissues and organs. Recent experimental evidence has emphasized the fundamental role of tissue growth in expanding the expression domains of morphogens and their target genes, in generating morphogen gradients and in modulating the response of cells to morphogens. Moreover, the classic view of how morphogens, particularly through their concentration gradient, regulate tissue size during development has been revisited recently. In this review, we discuss how morphogens and tissue growth affect each other, and we attempt to integrate genetic and molecular evidence from vertebrate and invertebrate model systems to put forward the idea that the interaction between growth and morphogens is a general feature of highly proliferative tissues.     

The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis

Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi) machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1—with conserved functions in cell division and morphogenesis from plants to humans—as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system.     

APC dosage effects in tumorigenesis and stem cell differentiation

It is well established that concentration gradients of signaling molecules (the so-called "morphogens") organize and pattern tissues in developing animals. In particular, studies in Drosophila and different vertebrates have shown that gradients of the Wnt, Hedgehog (Hh) and transforming growth factor-beta (TGF-beta) families of morphogens play critical roles in limb patterning. Morphogens are often expressed in organizing centres and can act over a long range to coordinate the patterning of an entire field of cells. These observations imply that exposure to different concentrations of these diffusible factors may trigger differential cellular responses. In order to study these dosage-dependent Wnt/beta-catenin signaling effects, we have generated several hypomorphic mutant alleles at the mouse Apc locus and studied their cellular and phenotypic outcomes in stem cell renewal and differentiation, and in tumorigenesis. The results clearly show that Apc mutations differentially affect the capacity of stem cells to differentiate in a dosage-dependent fashion. Likewise, different Apc mutations (and the corresponding Wnt signaling dosages) confer different degrees of susceptibility to tumorigenesis in the corresponding mouse models. These results have implications for the understanding of the molecular and cellular basis of tumor initiation by defects in the Wnt pathway. We propose a model in which adult somatic stem cell compartments are characterized by tissue-specific beta-catenin threshold levels for cell proliferation, differentiation and apoptosis. Different APC mutations will result in different levels of beta-catenin signaling, thus conferring different degrees of tumor susceptibility in different tissues. Hence, beta-catenin dosage-dependent effects may not only explain how a single pathway is involved in the development and homeostasis of different tissues, but also its pleiotrophic role in tumorigenesis.     

Evolution of class III homeodomain-leucine zipper genes in streptophytes

Land plants underwent tremendous evolutionary change following the divergence of the ancestral lineage from algal relatives. Several important developmental innovations appeared as the embryophyte clade diversified, leading to the appearance of new organs and tissue types. To understand how these changes came about, we need to identify the fundamental genetic developmental programs that are responsible for growth, patterning, and differentiation and describe how these programs were modified and elaborated through time to produce novel morphologies. Class III homeodomain-leucine zipper (class III HD-Zip) genes, identified in the model plant Arabidopsis thaliana, provide good candidates for basic land plant patterning genes. We show that these genes may have evolved in a common ancestor of land plants and their algal sister group and that the gene family has diversified as land plant lineages have diversified. Phylogenetic analysis, expression data from nonflowering lineages, and evidence from Arabidopsis and other flowering plants indicate that class III HD-Zip genes acquired new functions in sporophyte apical growth, vascular patterning and differentiation, and leaf development. Modification of expression patterns that accompanied diversification of class III HD-Zip genes likely played an important role in the evolution of land plant form.     

Elucidating mechanisms underlying robustness of morphogen gradients

Morphogen gradients play a pivotal role in most phases of developmental patterning. To ensure proper patterning, reproducible gradients are established under diverse environmental conditions and genetic backgrounds. We refer to the capacity to buffer fluctuations in gene dosage or environmental conditions as 'robustness'. By theoretical analysis of mechanisms that facilitate robustness, it is possible to unravel the machinery responsible for generating the spatial distribution of morphogens.     

Functional aspects of cell patterning in aerial epidermis

Plants have evolved epidermal cells that have specialized functions as adaptations to life on land. Many of the functions of these specialized cells are dependent, to a significant extent, on their arrangement within the aerial epidermis. Considerable progress has been made over the past two years in understanding the patterning mechanisms of trichomes and stomata in Arabidopsis leaves at the molecular level. How universal are these patterning programmes, and how are they adjusted to meet the changing functions of specialized epidermal cells in different plant organs? In this review, we compare the patterning of stomata and trichomes in different plant species, describe environmental and developmental factors that alter cell patterning, and discuss how changes in patterning might relate to cell function. Patterning is an important aspect to the functioning of aerial epidermal cells, and a greater understanding of the processes that are involved will significantly enhance our understanding of how cellular activities are integrated in multicellular plants.