A computational framework for cortical microtubule dynamics in realistically shaped plant cells

Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells. It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes. This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules. To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed. To date, however, these models have been restricted to two dimensional planes or geometrically simple surfaces in three dimensions, which strongly limits their applicability as plant cells display a wide variety of shapes. This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array. Here we describe a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces. This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images. We validate the framework against expected or known results for the spherical and cubical geometry. We then use it to systematically study the individual contributions of global geometry, cell-edge induced catastrophes and cell-face induced stability to array organization in a cuboidal geometry. Finally, we apply our framework to analyze the highly non-trivial geometry of leaf pavement cells of Arabidopsis thaliana, Nicotiana benthamiana and Hedera helix. We show that our simulations can predict multiple features of the microtubule array structure in these cells, revealing, among others, strong constraints on the orientation of division planes

Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis

Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway

Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control

The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta. Genetic interaction between the RBR-silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity

Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development

Desert plants have developed mechanisms for adapting to hostile desert conditions, yet these mechanisms remain poorly understood. Here, we describe two unique modes used by desert date palms (Phoenix dactylifera L.) to protect their meristematic tissues during early organogenesis. We used X-ray micro-computed tomography combined with high-resolution tissue imaging to reveal that, after germination, development of the embryo pauses while it remains inside a dividing and growing cotyledonary petiole. Transcriptomic and hormone analyses show that this developmental arrest is associated with the low expression of development-related genes and accumulation of hormones that promote dormancy and confer resistance to stress. Furthermore, organ-specific cell type mapping demonstrates that organogenesis occurs inside the cotyledonary petiole, with identifiable root and shoot meristems and their respective stem cells. The plant body emerges from the surrounding tissues with developed leaves and a complex root system that maximizes efficient nutrient and water uptake. We further show that, similar to its role in Arabidopsis thaliana, the SHORT-ROOT (SHR) homologue from date palms functions in maintaining stem cell activity and promoting formative divisions in the root ground tissue. Our findings provide insight into developmental programs that confer adaptive advantages in desert plants that thrive in hostile habitats

The apocarotenoid metabolite zaxinone regulates growth and strigolactone biosynthesis in rice

Strigolactone and abscisic acid are carotenoid-derived plant hormones. Here the authors describe the identification of zaxinone, a further apocarotenoid metabolite, which down-regulates strigolactone content and is required for normal growth and development in rice

Aspectos moleculares de la respuesta defensiva de las plantas a la formación de la simbiosis micorriza arbuscular

La simbiosis micorriza arbuscular (MA) es una de las asociaciones mutualistas más extendidas del reino vegetal. Esta simbiosis está formada por raíces de plantas y hongos del suelo. El establecimiento de la misma supone una serie de ventajas ecológicas, y fisiológicas para ambos asociados. Si bien la simbiosis mutualista MA es una de las más extendidas en el reino vegetal, también es de las más desconocidas a nivel de funcionamiento y regulación, principalmente debido a la incapacidad del hongo arbuscular de crecer en condiciones de laboratorio en ausencia de la planta hospedadora. Por tanto pocos son los conocimientos que se tienen acerca de los mecanismos moleculares de reconocimiento, establecimiento y funcionamiento de la simbiosis MA. Nuestros estudios se centraron en la interacción raíz- hongo arbuscular durante las primeras etapas de econocimiento y contacto del hongo arbuscular Glomus mosseae con la raíz hospedadora, detectándose una respuesta de tipo defensivo débil y transitoria en la raíz, que se puso de manifiesto por el incremento de la expresión de genes Ltp y Pal en las raíces de plantas de arroz y de actividades catalasa y ascorbato peroxidasa en raíces de plantas de tabaco. Los incrementos transitorios detectados coinciden con la etapa de desarrollo del hongo arbuscular en la rizosfera y formación de los apresorios trás contacto con la raíz. El análisis de la acumulación de ácido salicílico durante las etapas iniciales de la interacción, mostró una inducción de los niveles en raíz colonizada. Dicha inducción es transitoria y débil, en comparación con la obtenida frente a microorganismos patógenos, y coincide en el tiempo con la inducción de la expresión de genes Ltp y Pal. La aplicación exógena de ácido salicílico como agente inductor de la expresión de genes de defensa retrasa el proceso de la colonización de la raíz en plantas de arroz y guisante, aunque no afecta el porcentaje de raíz colonizada al final del experimento, ni el número de puntos de entrada del hongo en la raíz, indicando un efecto transitorio sobre la capacidad de penetración del hongo, y no sobre el desarrollo del mismo en el interior de la raíz. Nuestra investigación ha puesto de manifiesto la relación directa entre la resistencia de la micorrización y nodulación provocada por la mutación del gen simbiótico sym 30, y la acumulación de ácido salicílico en la raíz de plantas de guisante inoculadas con el hongo arbuscular Glomus mosseae o la bacteria Rhizobium leguminosarum. Dicha acumulación no se detectó en la interacción con la bacteria patógena Pseudomonas syringae. Estos hechos confirman la participación de genes simbióticos en el control de la respuesta defensiva de la planta frente a microorganismos simbióticos mutualistas. Utilizando la técnica DDRT-PCR hemos detectado una expresión génica diferencial de la planta durante el proceso de la colonización fúngica. El estudio y la caracterización de los ADNcs obtenidos en este análisis diferencial nos permitirá estudiar y clonar los genes ferenciales, así como analizar su función durante el proceso de establecimiento de la simbiosisUniversidad de Granada, Departamento de Biología Vegetal. Leída 20-07-9

A blast from the past: Understanding stem cell specification in plant roots using laser ablation

In the Arabidopsis root, growth is sustained by the meristem. Signalling from organiser cells, also termed the quiescent centre (QC), is essential for the maintenance and replenishment of the stem cells. Here, we highlight three publications from the founder of the concept of the stem cell niche in Arabidopsis and a pioneer in unravelling regulatory modules governing stem cell specification and maintenance, as well as tissue patterning in the root meristem: Ben Scheres. His research has tremendously impacted the plant field. We have selected three publications from the Scheres legacy, which can be considered a breakthrough in the field of plant developmental biology. van den Berg et al. (1995) and van den Berg et al. (1997) uncovered that positional information-directed patterning. Sabatini et al. (1999), discovered that auxin maxima determine tissue patterning and polarity. We describe how simple but elegant experimental designs have provided the foundation of our current understanding of the functioning of the root meristem