Mutual repression enhances the steepness and precision of gene expression boundaries

Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular, gene expression boundaries are robust not only against intra-embryonic fluctuations such as noise in gene expression and protein diffusion, but also against embryo-to-embryo variations in the morphogen gradients, which provide positional information to the differentiating cells. How development is robust against intra- and inter-embryonic variations is not understood. A common motif in the gene regulation networks that control embryonic development is mutual repression between pairs of genes. To assess the role of mutual repression in the robust formation of gene expression patterns, we have performed large-scale stochastic simulations of a minimal model of two mutually repressing gap genes in Drosophila, hunchback (hb) and knirps (kni). Our model includes not only mutual repression between hb and kni, but also the stochastic and cooperative activation of hb by the anterior morphogen Bicoid (Bcd) and of kni by the posterior morphogen Caudal (Cad), as well as the diffusion of Hb and Kni between neighboring nuclei. Our analysis reveals that mutual repression can markedly increase the steepness and precision of the gap gene expression boundaries. In contrast to other mechanisms such as spatial averaging and cooperative gene activation, mutual repression thus allows for gene-expression boundaries that are both steep and precise. Moreover, mutual repression dramatically enhances their robustness against embryo-to-embryo variations in the morphogen levels. Finally, our simulations reveal that diffusion of the gap proteins plays a critical role not only in reducing the width of the gap gene expression boundaries via the mechanism of spatial averaging, but also in repairing patterning errors that could arise because of the bistability induced by mutual repression.     

Formation of morphogen gradients in the Drosophila wing.

Patterning of multicellular fields requires mechanisms to coordinate developmental decisions made by populations of cells. Evidence is accumulating that the necessary information is provided by localized sources of secreted signalling proteins which act as morphogens. We review evidence that Wingless, Dpp and Hedgehog proteins act as morphogens in the developing wing of Drosophila and discuss recent work illustrating that signalling helps to shape their activity gradients by regulating ligand distribution and by modulating the responsiveness of target cells. These studies suggest that there is more to being a morphogen than formation of a ligand gradient by passive diffusion.     

Proteolytic regulatory mechanisms in the formation of extracellular morphogen gradients

Growth factors are secreted into the extracellular space, where they encounter soluble inhibitors, extracellular matrix glycoproteins and proteoglycans, and proteolytic enzymes that can each modulate the spatial distribution, activity state, and receptor interactions of these signaling molecules. During development, morphogenetic gradients of these growth factors pattern fields of cells responsive to different levels of signaling, creating such structures as the branched pattern of airways and vasculature, and the arrangement of digits in the hand. This review focuses specifically on the roles of proteolytic enzymes and their regulators in the generation of such activity gradients. Evidence from Drosophila developmental pathways provides a detailed understanding of general mechanisms underlying proteolytic control of morphogen gradients, while recent studies of several mammalian growth factors illustrate the relevance of this proteolytic control to human development and disease.     

Understanding morphogen gradients: a problem of dispersion and containment

Protein morphogens are instructive signals that regulate growth and patterning of tissues and organs. They form long-range, dynamic gradients by moving from regions of high concentration (producing cells) to regions of low concentration (the adjacent, nonproducing developmental field). Since morphogen activity must be limited to the adjacent target field, we want to understand both how signaling proteins move and how their dispersion is restricted. We consider the variety of settings for long-range morphogen systems in Drosophila. In the early embryo, morphogens appear to disperse by free diffusion, and impermeable membranes physically constrain them. However, at later stages, containment is achieved without physical barriers. We argue that in the absence of constraining barriers, gradient-generating dispersion of morphogens cannot be achieved by passive diffusion and that other mechanisms for distribution must be considered.     

Shaping BMP morphogen gradients in the Drosophila embryo and pupal wing

In the early Drosophila embryo, BMP-type ligands act as morphogens to suppress neural induction and to specify the formation of dorsal ectoderm and amnioserosa. Likewise, during pupal wing development, BMPs help to specify vein versus intervein cell fate. Here, we review recent data suggesting that these two processes use a related set of extracellular factors, positive feedback, and BMP heterodimer formation to achieve peak levels of signaling in spatially restricted patterns. Because these signaling pathway components are all conserved, these observations should shed light on how BMP signaling is modulated in vertebrate development.     

Improving the understanding of cytoneme-mediated morphogen gradients by in silico modeling

Morphogen gradients are crucial for the development of organisms. The biochemical properties of many morphogens prevent their extracellular free diffusion, indicating the need of an active mechanism for transport. The involvement of filopodial structures (cytonemes) has been proposed for morphogen signaling. Here, we describe an in silico model based on the main general features of cytoneme-meditated gradient formation and its implementation into Cytomorph, an open software tool. We have tested the spatial and temporal adaptability of our model quantifying Hedgehog (Hh) gradient formation in two Drosophila tissues. Cytomorph is able to reproduce the gradient and explain the different scaling between the two epithelia. After experimental validation, we studied the predicted impact of a range of features such as length, size, density, dynamics and contact behavior of cytonemes on Hh morphogen distribution. Our results illustrate Cytomorph as an adaptive tool to test different morphogen gradients and to generate hypotheses that are difficult to study experimentally.     

The hedgehog morphogen and gradients of cell affinity in the abdomen of Drosophila

The adult abdomen of Drosophila is a chain of anterior (A) and posterior (P) compartments. The engrailed gene is active in all P compartments and selects the P state. Hedgehog enters each A compartment across both its anterior and posterior edges; within A its concentration confers positional information. The A compartments are subdivided into an anterior and a posterior domain that each make different cell types in response to Hedgehog. We have studied the relationship between Hedgehog, engrailed and cell affinity. We made twin clones and measured the shape, size and displacement of the experimental clone, relative to its control twin. We varied the perceived level of Hedgehog in the experimental clone and find that, if this level is different from the surround, the clone fails to grow normally, rounds up and sometimes sorts out completely, becoming separated from the epithelium. Also, clones are displaced towards cells that are more like themselves: for example groups of cells in the middle of the A compartment that are persuaded to differentiate as if they were at the posterior limit of A, move posteriorly. Similarly, clones in the anterior domain of the A compartment that are forced to differentiate as if they were at the anterior limit of A, move anteriorly. Quantitation of these measures and the direction of displacement indicate that there is a U-shaped gradient of affinity in the A compartment that correlates with the U-shaped landscape of Hedgehog concentration. Since affinity changes are autonomous to the clone we believe that, normally, each cell's affinity is a direct response to Hedgehog. By removing engrailed in clones we show that A and P cells also differ in affinity from each other, in a manner that appears independent of Hedgehog. Within the P compartment we found some evidence for a U-shaped gradient of affinity, but this cannot be due to Hedgehog which does not act in the P compartment.     

Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis

Summary Spore formation in the Gram-positive bacterium Bacillus subtilis is a last resort adaptive response to starvation. To initiate sporulation, the key regulator in this process, Spo0A, needs to be activated by the so-called phosphorelay. Within a sporulating culture of B. subtilis, some cells initiate this developmental program, while other cells do not. Therefore, initiation of sporulation appears to be a regulatory process with a bistable outcome. Using a single cell analytical approach, we show that the autostimulatory loop of spo0A is responsible for generating a bistable response resulting in phenotypic variation within the sporulating culture. It is demonstrated that the main function of RapA, a phosphorelay phosphatase, is to maintain the bistable sporulation gene expression. As rapA expression is quorum regulated, it follows that quorum sensing influences sporulation bistability. Deletion of spo0E, a phosphatase directly acting on Spo0A approximately P, resulted in abolishment of the bistable expression pattern. Artificial induction of a heterologous Rap phosphatase restored heterogeneity in a rapA or spo0E mutant. These results demonstrate that with external phosphatases, B. subtilis can use the phosphorelay as a tuner to modulate the bistable outcome of the sporulating culture. This shows that B. subtilis employs multiple pathways to maintain the bistable nature of a sporulating culture, stressing the physiological importance of this phenomenon.     

Longitudinal gradients of collagen and elastin gene expression in the porcine aorta

The physical and chemical properties of the mammalian aorta are known to vary as a function of distance from the heart. These properties are highly dependent collagen and elastic fibers. In order to evaluate the mechanisms which regulate the accumulation of these two connective tissue proteins, gene expression was evaluated at both the biosynthetic and messenger RNA levels. Short-term (3 h) explant cultures of the medial portion of four segments of the descending aorta in newborn pigs were incubated in the presence of [3H] proline. Collagen production was quantified by collagenase digestion and elastin production was determined by immunoprecipitation. Between the conus arteriosus and the bifurcation of the iliac arteries, relative collagen synthesis increased 2-fold (from 5.8 to 12.0% of total protein synthesis), while relative elastin synthesis declined 10-fold (from 16.4 to 1.6% of total protein synthesis). Similarly, collagen production increased more than 7-fold (from 6.7 to 49.8 X 10(3) molecules/cell/h) while elastin production was reduced more than 3-fold (from 71.8 to 21.0 X 10(3) molecules/cell/h) along this developmental gradient. Elastin synthesis appeared to be controlled to a significant extent by the availability of elastin mRNA, since both cell-free translation and molecular hybridization to a cloned elastin gene probe showed gradients of elastin gene expression. Similarly, collagen synthesis was apparently regulated, at least in part, by an inverse gradient of collagen mRNA, as measured with a cloned cDNA for the pro-alpha 1(I) collagen gene. Marked changes in the amount of non-elastin protein synthesis accompanied differentiation and accounted for larger changes in relative synthesis. These results suggest that the phenotype of the cells of the porcine artery wall is distinct in different regions of this organ at this developmental stage.     

Distinguishing graded and ultrasensitive signalling cascade kinetics by the shape of morphogen gradients in Drosophila

Recently, signalling gradients in cascades of two-state reaction-diffusion systems were described as a model for understanding key biochemical mechanisms that underlie development and differentiation processes in the Drosophila embryo. Diffusion-trapping at the exterior of the cell membrane triggers the mitogen-activated protein kinase (MAPK) cascade to relay an appropriate signal from the membrane to the inner part of the cytosol, whereupon another diffusion-trapping mechanism involving the nucleus reads out this signal to trigger appropriate changes in gene expression. Proposed mathematical models exhibit equilibrium distributions consistent with experimental measurements of key spatial gradients in these processes. A significant property of the formulation is that the signal is assumed to be relayed from one system to the next in a linear fashion. However, the MAPK cascade often exhibits nonlinear dose-response properties and the final remark of Berezhkovskii et al. (2009) is that this assumption remains an important property to be tested experimentally, perhaps via a new quantitative assay across multiple genetic backgrounds. In anticipation of the need to be able to sensibly interpret data from such experiments, here we provide a complementary analysis that recovers existing formulae as a special case but is also capable of handling nonlinear functional forms. Predictions of linear and nonlinear signal relays and, in particular, graded and ultrasensitive MAPK kinetics, are compared.