Talking through walls: mechanisms of lateral root emergence in Arabidopsis thaliana.

Lateral roots are formed postembryonically and determine the final shape of the root system, a determinant of the plants ability to uptake nutrients and water. The lateral root primordia are initiated deep into the main root and to protrude out the primary root they have to grow through three cell layers. Recent findings have revealed that these layers are not merely a passive physical obstacle to the emergence of the lateral root but have an active role in its formation. Here, we review examples of communication between the lateral root primordium and the surrounding tissues, highlighting the importance of auxin-mediated growth coordination as well as cell and tissue mechanics for the morphogenesis of lateral roots

Cytoskeleton dynamics and cell remodelling during Arabidopsis thaliana lateral root development

Plants are characterized by an unparalleled ability to adapt to their environment by forming organs post-embryonically. In contrast to animal cells, plant cells are encaged in a rigid extracellular matrix, the cell wall, which glues cells tightly to their neighbours. The presence of the cell wall precludes cell migration and determines that plant morphogenesis relies on the ability of cells to control the direction of growth and the orientation of cell division. The microtubule and actin cytoskeletons play an essential role in the control of these processes. Cortical microtubules guide the deposition of cellulose fibrils in the cell wall and in consequence dictate the shape and growth direction of the cell. Actin is essential for the establishment and maintenance of cell polarity and together with microtubules orchestrates cell division. The root system is formed by the continuous growth of root tips and branching of lateral roots. This enables anchoring and efficient absorption of water and nutrients. The branching of lateral root starts with the coordinated division of two pericycle founder cells located in the outer most layer of the main root vasculature. During this phase, called lateral root initiation (LRI), founder cells swell synchronously and their nuclei migrate towards the common cell wall Once nuclei are asymmetrically localized, founder cells divide asymmetrically originating two small daughter cells in the centre and two long daughter cells at the flanks. In this work, we combined cytoskeleton tissue-specific markers and confocal live imaging to determine the role of the cytoskeleton in the coordination of the swelling and nuclear migration of founder cells during LRI. We observed that founder cells expand more in the central domain than in the periphery, a process amplified by the asymmetric positioning of the nucleus and pursued after the first asymmetric cell division (ACD). We observed that after ACD, microtubules reorganise in a parallel array at the periphery and remain more isotropic in the central domain. Genetic and pharmacological perturbation of microtubule organization, support a model in which the graded organization of microtubules constraints radial expansion at the periphery and allow fast expansion of the central cells. We detected that before cell division actin bundles reorganize in a polarized mesh around the nucleus. Pharmacological disruption of actin network revealed that actin is essential for the migration of the nucleus, the asymmetry of cell division and cell expansion. Auxin is an essential regulator of LRI that controls in particular the expression of LBD16, a transcription factor involved in the polar migration of nuclei during LRI. Expression of the repressor LBD16-SRDX abolishes nuclear migration and asymmetric cell division. We observed that cytoskeleton polarity and organization are disrupted in the LBD16-SRDX background, where asymmetric cell expansion is also impaired. After initiation, founder cells divide and expand to form a dome shaped primordium (LRP) in response to the spatial accommodation of the overlaying endodermis. In a second part of this work, we observed that disturbing microtubule dynamics hinders the spatial remodelling of the endodermis and delays the growth of the LRP. We found that microtubule organization in the endodermis is dependent on SHY2-mediated auxin signalling and shows a cell face-determined pattern. In conclusion, our results evidence the importance of cytoskeleton dynamics during LRI and the spatial accommodation of the endodermis and reveal a role for auxin signalling in these processes

EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation

In plants, postembryonic formation of new organs helps shape the adult organism. This requires the tight regulation of when and where a new organ is formed and a coordination of the underlying cell divisions. To build a root system, new lateral roots are continuously developing, and this process requires the tight coordination of asymmetric cell division in adjacent pericycle cells. We identified EXPANSIN A1 (EXPA1) as a cell wall modifying enzyme controlling the divisions marking lateral root initiation. Loss of EXPA1 leads to defects in the first asymmetric pericycle cell divisions and the radial swelling of the pericycle during auxin-driven lateral root formation. We conclude that a localized radial expansion of adjacent pericycle cells is required to position the asymmetric cell divisions and generate a core of small daughter cells, which is a prerequisite for lateral root organogenesis

Accurate and versatile 3D segmentation of plant tissues at cellular resolution

Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on fixed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, acquisition settings even on non plant samples. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface

Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis

Precise coordination between cells and tissues is essential for differential growth in plants. During lateral root formation in Arabidopsis thaliana, the endodermis is actively remodeled to allow outgrowth of the new organ. Here, we show that microtubule arrays facing lateral root founder cells display a higher order compared to arrays on the opposite side of the same cell, and this asymmetry is required for endodermal remodeling and lateral root initiation. We identify that MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is necessary for the establishment of this spatially defined microtubule organization and endodermis remodeling and thus contributes to lateral root morphogenesis. We propose that MAP70-5 and cortical microtubule arrays in the endodermis integrate the mechanical signals generated by lateral root outgrowth, facilitating the channeling of organogenesis

Cytoskeleton Dynamics Are Necessary for Early Events of Lateral Root Initiation in Arabidopsis

How plant cells re-establish differential growth to initiate organs is poorly understood. Morphogenesis of lateral roots relies on the asymmetric cell division of initially symmetric founder cells. This division is preceded by the tightly controlled asymmetric radial expansion of these cells. The cellular mechanisms that license and ensure the coordination of these events are unknown. Here, we quantitatively analyze microtubule and F-actin dynamics during lateral root initiation. Using mutants and pharmacological and tissue-specific genetic perturbations, we show that dynamic reorganization of both microtubule and F-actin networks is necessary for the asymmetric expansion of the founder cells. This cytoskeleton remodeling intertwines with auxin signaling in the pericycle and endodermis in order for founder cells to acquire a basic polarity required for initiating lateral root development. Our results reveal the conservation of cell remodeling and polarization strategies between the Arabidopsis zygote and lateral root founder cells. We propose that coordinated, auxin-driven reorganization of the cytoskeleton licenses asymmetric cell growth and divisions during embryonic and post-embryonic organogenesis