Brassinosteroids role in arabidopsis root development : theoretical and experimental approaches

Abstract

This PhD thesis represents an advance in the present understanding of the spatiotemporal control of model plant Arabidopsis thaliana root growth and development. The size and structure of a living organism are tightly controlled by the coordination between several highly dynamic molecular and cellular processes, such as cell division, movement, growth and deformation. At tissue level, a mesoscopic description of the system and these processes can be used, in terms of mechanical forces and energy minimization (see (Hamant & Traas, 2010) for a review focused on plants). How cells decide to switch from a cellular process to another is a fundamental question to understand the growth and shape of an organ. Because of the thermal fluctuations and finite number of molecules involved in the molecular reactions, cells take presumably these decisions in a stochastic manner, which makes it challenging to understand how morphogenesis generates organs with characteristic shapes and sizes.

Plant roots grow due to cell division in the meristem and subsequent cell elongation up to terminal differentiation. The pleiotropic phenotypes of the short-root mutants available make it difficult to univocally assess which mechanism sets the transition from elongation to final differentiation. To elucidate it, in this thesis we use a novel approach based on the quantitative information associated to the phenotypic variability of wild type roots together with computational modeling of different mechanisms.

In Chapter 1 we introduced the already published work in the field of root and meristem growth, at experimental and computational level.

In Chapter 2 we have employed theoretical and computational models to analyze individual isogenic Arabidopsis seedlings and to quantify their heterogeneity, which we have quantified, together with their mean values. The quantification of heterogeneity has been crucial since it allowed the identification of dynamical mechanisms involved in Arabidopsis root growth. By analyzing these mechanisms in WT plants and Brassinosteroids (BRs) mutants, we found that growth defects in the BRs loss of function mutant are generated by defects related to cell differentiation.

To deepen into this result, in Chapter 3 we investigated the mechanism through which cells decide to differentiate and achieve their final length. In this sense, we adopted a computational approach, combined with plant variability analysis, to test three putative mechanisms: Ruler (Band et al, 2012; De Vos et al, 2014), Timer (De Vos et al, 2014; Mähönen et al, 2014) and Sizer (Grieneisen et al, 2012). We compared the simulated

data, based on the values extracted in Chapter 2, with experiments, and we found that Arabidopsis thaliana primary root uses a Sizer mechanism based on measuring cell sizes for final cell differentiation. We show this mechanism translates into specific correlations among phenotypic traits and explains why root growth is proportional to the meristem activity and displays mature cells of stereotyped length. We challenged our model by evaluating such correlations in a well-known BR signaling short-root mutant. We further show that BR signaling at the meristem is sufficient to recover some of the correlation slopes and hence root growth, yet it alters the mechanism. Together, our results establish a theoretical quantitative framework for stationary root growth and underscore the value of using computational modeling together with quantitative data.

In Chapter 4 we analyzed the coupling between meristematic activity and telomere length by applying a novel quantitative fluorescence in situ hybridization to measure telomere length with tissue resolution in the primary root. The implementation of a new image analysis protocol contributed to revealing a telomere distribution map, with telomere length gradients along the meristem, and the longest telomeres localized in the stem cell niche (Gonzalez-Garcia et al, 2015). We applied this method to WT plants, several generations of telomerase deficient mutants, mutants with larger telomeres and cell differentiation mutants. Furthermore, we generated transgenic plants to check the localization of telomerase and we evaluated the relationship between telomere length and resistance to DNA damage. We also evaluated computationally the telomere distributions observed in WT and telomerase deficient mutants and we simulated the telomere dynamics which can generate such distributions.

The conclusions of this thesis were contextualized in Chapter 5.

El tamaño y la estructura de un organismo vivo son el resultado de una coordinación entre procesos moleculares y celulares, altamente dinámicos, como la división, el movimiento, el crecimiento y la deformación. A nivel de tejido se puede usar una descripción mesoscópica del sistema y estos procesos, habitualmente en términos de fuerzas mecánicas y minimización de la energía (dirigirse a (Hamant & Traas, 2010) para una revisión sobre plantas). Por tanto, la morfogénesis y formación de órganos en Eucariotas son investigadas tanto por la Biología de desarrollo, como por la Física de la materia blanda (Cross & Greenside, 2009; Cross & Hohenberg, 1993; Murray, 2002). El crecimiento global de una planta es fuertemente relacionado con el crecimiento y desarrollo de su raíz. Las raíces crecen debido a sucesivas divisiones celulares en el meristemo, seguidas por elongación y diferenciación celular. Para poder estudiar el desarrollo de la raíz es imprescindible conocer qué determina a las células tomar las decisiones de parar de dividir y elongarse o parar de elongarse y diferenciarse. Debido a las fluctuaciones térmicas y el número finito de moléculas que participan en las reacciones moleculares, es de esperar que estas decisiones no son tomadas por todas las células a la vez, sino de una manera estocástica, lo que hace dificil entender cómo la morfogénesis basada en un comportamiento celular estocástico puede generar formas y tamaños característicos de órganos.

En este contexto, esta tesis usa modelos matemáticos para cuantificar y generar predicciones sobre la dinámica de crecimiento de la raíz de Arabidopsis thaliana, que han sido testeadas mediante un abordaje experimental. En el Capítulo 2 de esta tesis hemos diseñado un marco teórico para describir el crecimiento estacionario de la raíz y hemos analizado la variabilidad existente entre raíces isogénicas. En el Capítulo 3 hemos usado un modelo matemático para investigar el mecanismo que las células usan para decidir cuándo parar de elongarse y adquirir su tamaño final. Basándonos en las predicciones de este modelo, hemos analizado la variabilidad intrínseca de las plantas silvestres y hemos identificado relaciones específicas entre los parámetros de crecimiento, que nos ayudaron a descartar posibles modelos. En el Capítulo 4 hemos cuantificado la longitud telomérica en las células de la raíz y evaluado funcionalidades biológicas. Nuestro análisis mostró una distribución heterogénea, que impulsó la

modelización matemática de la dinámica telomérica, basada en las fluctuaciones y el comportamiento dinámico de la longitud telomérica.