, provides an intuitively plausible interpretation of the data, but raises questions of whether the proposed mechanism is, in fact, capable of producing the observed temporal and spatial patterns, is robust, can start de novo, and can account for phyllotactic transitions, such as the frequently observed transition from decussate to spiral phyllotaxis. To answer these questions, we created a computer simulation model based on data described previously or in this paper and reasonable hypotheses. The model reproduces, within the standard error, the divergence angles measured in Arabidopsis seedlings and the effects of selected experimental manipulations. It also reproduces distichous, decussate, and tricussate patterns. The model thus offers a plausible link between molecular mechanisms of morphogenesis and the geometry of phyllotaxis.active transport ͉ auxin ͉ PIN ͉ polarity ͉ computer simulation W ithin the variety of phyllotactic patterns found in nature, the most intriguing and, at the same time, the most prevalent is the spiral phyllotactic pattern characterized by the arrangement of organs into conspicuous spirals (parastichies), where the numbers of parastichies are consecutive elements of the Fibonacci series. This pattern is related to the divergence angle between organs approximating the golden angle of 137.5°. In the entire world of developmental biology, phyllotaxis is perhaps the most striking example of a phenomenon that can only be described by using quantitative notions of geometry.The regularity and mathematical properties of spiral phyllotaxis have attracted the attention of biologists and mathematicians since the early 19th century. They proposed conceptual, mathematical, and computational models, which elucidated the geometric properties of spiral phyllotactic arrangements (1) and the emergence of phyllotactic patterns during plant development. This latter category of models was pioneered by Hofmeister (2) and Snow and Snow (3), who hypothesized that the creation of new primordia is inhibited by the proximity of older primordia. New primordia, therefore, can be formed only at a certain minimal distance from the old ones. This general hypothesis has subsequently been refined into a number of computational models, postulating and exploring different types of inhibitory mechanisms such as geometric spacing (4), physical forces (5, 6), and chemical signals (7,8).In the absence of molecular data, the proposed mechanisms were more or less abstract. Recent experiments, however, provided an insight into the molecular processes involved in phyllotaxis, pointing to the central role of active transport of the plant hormone auxin. When shoot apices were cultivated in the presence of auxin transport inhibitors, the induction of lateral organs was blocked, and the apices grew vigorously as radially symmetric structures. Application of the natural auxin indole-3-acetic acid (IAA) to such pin-shaped meristems induced lateral primordia, with the size and position depending on the concentration and the position o...

We provide a comprehensive expression map of the different genes (TIR1/AFBs, ARFs and Aux/IAAs) involved in the signalling pathway regulating gene transcription in response to auxin in the shoot apical meristem (SAM).We demonstrate a relatively simple structure of this pathway using a high-throughput yeast two-hybrid approach to obtain the Aux/IAA-ARF full interactome.The topology of the signalling network was used to construct a model for auxin signalling and to predict a role for the spatial regulation of auxin signalling in patterning of the SAM.We used a new sensor to monitor the input in the auxin signalling pathway and to confirm the model prediction, thus demonstrating that auxin signalling is essential to create robust patterns at the SAM.

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One of the most striking features of plant architecture is the regular arrangement of leaves and flowers around the stem, known as phyllotaxis. Peaks in concentration of the plant hormone auxin, generated by the polar localization of the PIN1 auxin efflux carrier, provide the instructive signal for primordium initiation. This mechanism generates the spacing between neighboring primordia, which results in regular phyllotaxis. Studies of the role of auxin transport in phyllotactic patterning have focused on PIN1-mediated efflux. Recent computer simulations indicate an additional role for transporter-mediated auxin uptake. Mutations in the AUX1 auxin influx carrier have not, however, been reported to cause an aerial phenotype. Here, we study the role of AUX1 and its paralogs LAX1, LAX2, and LAX3. Analysis of the quadruple mutant reveals irregular divergence angles between successive primordia. A highly unusual aspect of the phenotype is the occurrence of clusters of primordia, in violation of classical theory. At the molecular level, the sharp peaks in auxin levels and coordinated PIN polarization are reduced or lost. In addition, the increased penetrance of the phenotype under short-day conditions suggests that the AUX LAX transporters act to buffer the PIN-mediated patterning mechanism against environmental or developmental influences.

In Arabidopsis, lateral root primordia (LRPs) originate from pericycle cells located deep within the parental root and have to emerge through endodermal, cortical, and epidermal tissues. These overlaying tissues place biomechanical constraints on the LRPs that are likely to impact their morphogenesis. This study probes the interplay between the patterns of cell division, organ shape, and overlaying tissues on LRP morphogenesis by exploiting recent advances in live plant cell imaging and image analysis. Our 3D/4D image analysis revealed that early stage LRPs exhibit tangential divisions that create a ring of cells corralling a population of rapidly dividing cells at its center. The patterns of division in the latter population of cells during LRP morphogenesis are not stereotypical. In contrast, statistical analysis demonstrated that the shape of new LRPs is highly conserved. We tested the relative importance of cell division pattern versus overlaying tissues on LRP morphogenesis using mutant and transgenic approaches. The double mutant aurora1 (aur1) aur2 disrupts the pattern of LRP cell divisions and impacts its growth dynamics, yet the new organ's dome shape remains normal. In contrast, manipulating the properties of overlaying tissues disrupted LRP morphogenesis. We conclude that the interaction with overlaying tissues, rather than the precise pattern of divisions, is most important for LRP morphogenesis and optimizes the process of lateral root emergence.lateral root development | plant morphogenesis | biomechanical regulation | statistical shape analysis | Arabidopsis thaliana I n contrast to animals, only the basic blueprint of the plant body plan is laid out during embryogenesis. Instead, the majority of plant organs are formed postembryonically. In some instances, organ formation can occur deep within another organ, as is the case for lateral roots (1, 2). In addition, plant cells are constrained by rigid walls; hence, cell migration cannot occur. Instead, plant morphogenesis relies on two mechanisms: oriented cell division and anisotropic growth (3, 4). For example, during embryogenesis, cells exhibit a highly synchronized program of expansion and division (5). How cell division, cell shape, and overlaying tissues interact during plant organ morphogenesis is currently unclear.Lateral roots are derived from cell division events deep within the primary root (1, 2). Pairs of pericycle cells in several adjacent files undergo a series of asymmetric formative divisions (reviewed in ref. 6). These periclinal (parallel) and anticlinal (perpendicular) divisions give birth to a lateral root primordium (LRP) that will develop further into a lateral root comprising a new root meristem. LRP formation in Arabidopsis was first described in a pioneering study 14 years ago (7) that proposed a seven-stage taxonomy of LRP development on the basis of 2D observations of cell layer numbers that still forms the basis of all studies describing LRP development in Arabidopsis.Recent advances in live biological imaging and image ...

A large number of genes involved in lateral root (LR) organogenesis have been identified over the last decade using forward and reverse genetic approaches in Arabidopsis thaliana. Nevertheless, how these genes interact to form a LR regulatory network largely remains to be elucidated. In this study, we developed a time-delay correlation algorithm (TDCor) to infer the gene regulatory network (GRN) controlling LR primordium initiation and patterning in Arabidopsis from a time-series transcriptomic data set. The predicted network topology links the very early-activated genes involved in LR initiation to later expressed cell identity markers through a multistep genetic cascade exhibiting both positive and negative feedback loops. The predictions were tested for the key transcriptional regulator AUXIN RESPONSE FACTOR7 node, and over 70% of its targets were validated experimentally. Intriguingly, the predicted GRN revealed a mutual inhibition between the ARF7 and ARF5 modules that would control an early bifurcation between two cell fates. Analyses of the expression pattern of ARF7 and ARF5 targets suggest that this patterning mechanism controls flanking and central zone specification in Arabidopsis LR primordia.

Lateral root formation is an important determinant of root system architecture. In Arabidopsis, lateral roots originate from pericycle cells, which undergo a program of morphogenesis to generate a new lateral root meristem. Despite its importance for root meristem organization, the onset of quiescent center (QC) formation during lateral root morphogenesis remains unclear. Here, we used live 3D confocal imaging to monitor cell organization and identity acquisition during lateral root development. Our dynamic observations revealed an early morphogenesis phase and a late meristem formation phase as proposed in the bi-phasic growth model. Establishment of lateral root QCs coincided with this developmental phase transition. QC precursor cells originated from the outer layer of stage II lateral root primordia, within which the SCARECROW (SCR) transcription factor was specifically expressed. Disrupting SCR function abolished periclinal divisions in this lateral root primordia cell layer and perturbed the formation of QC precursor cells. We conclude that de novo QC establishment in lateral root primordia operates via SCR-mediated formative cell division and coincides with the developmental phase transition.

Activated forms of jasmonic acid (JA) are central signals coordinating plant responses to stresses, yet tools to analyse their spatial and temporal distribution are lacking. Here we describe a JA perception biosensor termed Jas9-VENUS that allows the quantification of dynamic changes in JA distribution in response to stress with high spatiotemporal sensitivity. We show that Jas9-VENUS abundance is dependent on bioactive JA isoforms, the COI1 co-receptor, a functional Jas motif and proteasome activity. We demonstrate the utility of Jas9-VENUS to analyse responses to JA in planta at a cellular scale both quantitatively and dynamically. This included using Jas9-VENUS to determine the cotyledon-to-root JA signal velocities upon wounding, revealing two distinct phases of JA activity in the root. Our results demonstrate the value of developing quantitative sensors such as Jas9-VENUS to provide high-resolution spatiotemporal data about hormone distribution in response to plant abiotic and biotic stresses.