Evolution du régulateur floral LEAFY dans la lignée verte

LEAFY (LFY) is a unique transcription factor, highly conserved within land plants. LFY directly regulates a set of genes participating in floral development in angiosperms (flowering plants), but its role in the other groups of land plants is unknown, except in the moss Physcomitrella patens where the LFY ortholog (PpLFY) regulates the first cell division in the zygote. PpLFY does not bind to the same DNA sequences as LFY from Arabidopsis thaliana, in spite of the very high degree of conservation of their DNA binding domains. Thus, it appears that the properties of LFY have changed during evolution ; the goal of my thesis was to find out if such changes had occurred frequently in land plants, and what are their origins and consequences on target genes regulation. I performed SELEX experiments on LFY orthologs from all land plants, which revealed that their DNA binding specificty was highly conserved, except in the case of PpLFY. These results allowed us to build an accurate biophysical model to predict LFY binding on DNA fragments at a genomic level, which we applied on the evolution of the regulation of key target genes by LFY. We were able to predict the regulation of the floral gene AGAMOUS by LFY in various angiosperm species, et we could also show that LFY was very likely regulating gymnosperm orthologs of genes involved in floral organ identity, even before the appearance of the flower. The change in DNA binding specificity observed for PpLFY led us to study more precisely the consequences of this change for the regulation of target genes : for this, I initiated bioinformatic and experimental work in P. patens. Finally, to understand how this change in DNA binding specificity had occurred during evolution, we looked for the ancestor of LFY and found out that LFY already existed in green algae. We are currently investigating the ancestral specificity of LFY in these species.LEAFY (LFY) est un facteur de transcription unique et très conservé chez les plantes terrestres. Il contrôle le développement floral chez les angiospermes (plantes à fleurs), mais son rôle est encore mal connu chez toutes les autres plantes terrestres à l'exception de la mousse Physcomitrella patens où l'orthologue de LFY (PpLFY) est requis pour la première division cellulaire du zygote. PpLFY ne reconnaît pas les mêmes séquences d'ADN que LFY d'Arabidopsis thaliana, malgré la très forte conservation de leurs domaines de liaison à l'ADN. LFY semble donc avoir changé de propriétés au cours de l'évolution ; l'objectif de ma thèse a été de déterminer si de tels changements s'étaient produits fréquemment chez les plantes terrestres, et de comprendre leur origine et leur impact sur la régulation des gènes cibles de LFY. Pour cela, j'ai étudié la spécificité de liaison à l'ADN des orthologues de LFY chez les grands groupes de plantes terrestres par des expériences de SELEX, et cette spécificité s'est révélée très fortement conservée, excepté dans le cas de PpLFY. Ces résultats nous ont permis de construire un modèle biophysique performant pour prédire la liaison de LFY à l'échelle génomique, ce que nous avons appliqué à l'étude de l'évolution de la régulation de quelques gènes clés par LFY. Nous avons ainsi pu prédire la régulation du gène floral AGAMOUS par LFY chez différentes espèces angiospermes, et nous avons pu montrer que LFY régulait très vraisemblablement les orthologues des gènes d'identité florale chez les gymnospermes, c'est-à-dire avant l'apparition de la fleur. La divergence de spécificité de PpLFY nous a poussés à étudier les gènes cibles de PpLFY : pour cela, j'ai initié des approches bioinformatiques et expérimentales chez P. patens. Enfin, pour comprendre comment ce changement de spécificité s'est déroulé au cours de l'évolution, nous nous sommes penchés sur l'ancêtre de LFY et avons découvert que LFY était déjà présent chez les algues vertes. Des études pour déterminer la spécificité ancestrale de LFY chez ces espèces ont été initiées

How to Evolve a Perianth: A Review of Cadastral Mechanisms for Perianth Identity

The flower of angiosperms is considered to be a major evolutionary innovation that impacted the whole biome. In particular, two properties of the flower are classically linked to its ecological success: bisexuality and a differentiated perianth with sepals and petals. Although the molecular basis for floral organ identity is well understood in extant species and summarized in the famous ABC model, how perianth identity appeared during evolution is still unknown. Here we propose that cadastral mechanisms that maintain reproductive organ identities to the center of the flower could have supported perianth evolution. In particular, repressing B- and C-class genes expression toward the inner whorls of the flower, is a key process to isolate domains with sepal and petal identity in the outer whorls. We review from the literature in model species the diverse regulators that repress B- and C-class genes expression to the center of the flower. This review highlights the existence of both unique and conserved repressors between species, and possible candidates to investigate further in order to shed light on perianth evolution

BAXMC: a CEGAR approach to Max\#SAT

Max\#SAT is an important problem with multiple applications in security and program synthesis that is proven hard to solve. It is defined as: given a parameterized quantifier-free propositional formula compute parameters such that the number of models of the formula is maximal. As an extension, the formula can include an existential prefix. We propose a CEGAR-based algorithm and refinements thereof, based on either exact or approximate model counting, and prove its correctness in both cases. Our experiments show that this algorithm has much better effective complexity than the state of the art.Comment: FMCAD 2022, Oct 2022, Trente, Ital

Cell-Kinetics Based Calibration of a Multiscale Model of Structured Cell Populations in Ovarian Follicles

International audienceIn this paper, we present a strategy for tuning the parameters of a multiscale model of structured cell populations in which physiological mechanisms are embedded into the cell scale. This strategy allows one to cope with the technical difficulties raised by such models, that arise from their anchorage in cell biology concepts: localized mitosis, progression within and out of the cell cycle driven by time-and possibly unknown-dependent, and nonsmooth velocity coefficients. We compute different mesoscopic and macroscopic quantities from the microscopic unknowns (cell densities) and relate them to experimental cell kinetic indexes. We study the expression of reaching times corresponding to characteristic cellular transitions in a particle-like reduction of the original model. We make use of this framework to obtain an appropriate initial guess for the parameters and then perform a sequence of optimization steps subject to quantitative specifications. We finally illustrate realistic simulations of the cell populations in cohorts of interacting ovarian follicles. Introduction. In this paper, we deal with the question of the numerical calibration of an existing multiscale model of cell-structured populations in the physiological context of ovulation. This model was formulated as a system of weakly coupled, non conservative transport equations with controlled velocities and sink terms, where the unknowns are the cell densities in each follicle [9, 8]. A number of theoretical studies have established the well-posedness of the model [19], examined optimal control problems related to the ovulatory trajectories in the framework of hybrid optimal control theory [6], and studied the reachability of final states corresponding to either ovulatory or atretic cases in the framework of backwards reachable sets [8]. Implementation of the model in an efficient and reliable computing environment has involved the design of a finite-volume scheme dealing with the discontinuous coefficients [3], embedding this scheme within a dedicated adaptive mesh based on a multi-resolution approach [4], and implementing it on parallel architecture [2]. This has left the question of model calibration to biological specifications to be resolved. We have to face a generic, yet unsolved issue in parameter fitting for physiologically-oriented multiscale mathematical models: although mechanistic knowledge in molecular and cell biology is available on the lower scales, quantitative experimental data are rather available on the higher scales. In our case, the question is how to infer the parameters entering the microscopic functions (on the level of the follicular cells) from mesoscopic (on the level of the individual follicles, i.e. the number of follicular cells) or macroscopic (on the level of the populations of follicles) information. In addition, even on the macroscopic level, data remain rather scarce and are rarely obtained directly a

Seasonal regulation of petal number

International audienceFour petals characterize the flowers of most species in the Brassicaceae family, and this phenotype is generally robust to genetic and environmental variation. A variable petal number distinguishes the flowers of Cardamine hirsuta from those of its close relative Arabidopsis (Arabidopsis thaliana), and allelic variation at many loci contribute to this trait. However, it is less clear whether C. hirsuta petal number varies in response to seasonal changes in environment. To address this question, we assessed whether petal number responds to a suite of environmental and endogenous cues that regulate flowering time in C. hirsuta. We found that petal number showed seasonal variation in C. hirsuta, such that spring flowering plants developed more petals than those flowering in summer. Conditions associated with spring flowering, including cool ambient temperature, short photoperiod, and vernalization, all increased petal number in C. hirsuta. Cool temperature caused the strongest increase in petal number and lengthened the time interval over which floral meristems matured. We performed live imaging of early flower development and showed that floral buds developed more slowly at 15°C versus 20°C. This extended phase of floral meristem formation, coupled with slower growth of sepals at 15°C, produced larger intersepal regions with more space available for petal initiation. In summary, the growth and maturation of floral buds is associated with variable petal number in C. hirsuta and responds to seasonal changes in ambient temperature

Conservation versus divergence in LEAFY and APETALA functions between Arabidopsis thaliana and Cardamine hirsuta

International audienceA conserved genetic toolkit underlies the development of diverse floral forms among angiosperms. However, the degree of conservation vs divergence in the configuration of these gene regulatory networks is less clear. We addressed this question in a parallel genetic study between the closely related species Arabidopsis thaliana and Cardamine hirsuta. We identified leafy (lfy) and apetala1 (ap1) alleles in a mutant screen for floral regulators in C. hirsuta. C. hirsuta lfy mutants showed a complete homeotic conversion of flowers to leafy shoots, mimicking lfy ap1 double mutants in A. thaliana. Through genetic and molecular experiments, we showed that AP1 activation is fully dependent on LFY in C. hirsuta, by contrast to A. thaliana. Additionally, we found that LFY influences heteroblasty in C. hirsuta, such that loss or gain of LFY function affects its progression. Overexpression of UNUSUAL FLORAL ORGANS also alters C. hirsuta leaf shape in an LFY-dependent manner. We found that LFY and AP1 are conserved floral regulators that act nonredundantly in C. hirsuta, such that LFY has more obvious roles in floral and leaf development in C. hirsuta than in A. thaliana

Evolution of the floral regulator LEAFY in the green lineage

LEAFY (LFY) est un facteur de transcription unique et très conservé chez les plantes terrestres. Il contrôle le développement floral chez les angiospermes (plantes à fleurs), mais son rôle est encore mal connu chez toutes les autres plantes terrestres à l'exception de la mousse Physcomitrella patens où l'orthologue de LFY (PpLFY) est requis pour la première division cellulaire du zygote. PpLFY ne reconnaît pas les mêmes séquences d'ADN que LFY d'Arabidopsis thaliana, malgré la très forte conservation de leurs domaines de liaison à l'ADN. LFY semble donc avoir changé de propriétés au cours de l'évolution ; l'objectif de ma thèse a été de déterminer si de tels changements s'étaient produits fréquemment chez les plantes terrestres, et de comprendre leur origine et leur impact sur la régulation des gènes cibles de LFY. Pour cela, j'ai étudié la spécificité de liaison à l'ADN des orthologues de LFY chez les grands groupes de plantes terrestres par des expériences de SELEX, et cette spécificité s'est révélée très fortement conservée, excepté dans le cas de PpLFY. Ces résultats nous ont permis de construire un modèle biophysique performant pour prédire la liaison de LFY à l'échelle génomique, ce que nous avons appliqué à l'étude de l'évolution de la régulation de quelques gènes clés par LFY. Nous avons ainsi pu prédire la régulation du gène floral AGAMOUS par LFY chez différentes espèces angiospermes, et nous avons pu montrer que LFY régulait très vraisemblablement les orthologues des gènes d'identité florale chez les gymnospermes, c'est-à-dire avant l'apparition de la fleur. La divergence de spécificité de PpLFY nous a poussés à étudier les gènes cibles de PpLFY : pour cela, j'ai initié des approches bioinformatiques et expérimentales chez P. patens. Enfin, pour comprendre comment ce changement de spécificité s'est déroulé au cours de l'évolution, nous nous sommes penchés sur l'ancêtre de LFY et avons découvert que LFY était déjà présent chez les algues vertes. Des études pour déterminer la spécificité ancestrale de LFY chez ces espèces ont été initiées.LEAFY (LFY) is a unique transcription factor, highly conserved within land plants. LFY directly regulates a set of genes participating in floral development in angiosperms (flowering plants), but its role in the other groups of land plants is unknown, except in the moss Physcomitrella patens where the LFY ortholog (PpLFY) regulates the first cell division in the zygote. PpLFY does not bind to the same DNA sequences as LFY from Arabidopsis thaliana, in spite of the very high degree of conservation of their DNA binding domains. Thus, it appears that the properties of LFY have changed during evolution ; the goal of my thesis was to find out if such changes had occurred frequently in land plants, and what are their origins and consequences on target genes regulation. I performed SELEX experiments on LFY orthologs from all land plants, which revealed that their DNA binding specificty was highly conserved, except in the case of PpLFY. These results allowed us to build an accurate biophysical model to predict LFY binding on DNA fragments at a genomic level, which we applied on the evolution of the regulation of key target genes by LFY. We were able to predict the regulation of the floral gene AGAMOUS by LFY in various angiosperm species, et we could also show that LFY was very likely regulating gymnosperm orthologs of genes involved in floral organ identity, even before the appearance of the flower. The change in DNA binding specificity observed for PpLFY led us to study more precisely the consequences of this change for the regulation of target genes : for this, I initiated bioinformatic and experimental work in P. patens. Finally, to understand how this change in DNA binding specificity had occurred during evolution, we looked for the ancestor of LFY and found out that LFY already existed in green algae. We are currently investigating the ancestral specificity of LFY in these species

Unusual suspects in flower color evolution: The expression of phased small interfering RNAs caused monkeyflower color evolution

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Flower Development in the Solanaceae

International audienceFlower development is the process leading from a reproductive meristem to a mature flower with fully developed floral organs. This multi-step process is complex and involves thousands of genes in intertwined regulatory pathways; navigating through the FLOR-ID website will give an impression of this complexity and of the astonishing amount of work that has been carried on the topic. Our understanding of flower development mostly comes from the model species Arabidopsis thaliana, but numerous other studies outside of Brassicaceae have helped apprehend the conservation of these mechanisms in a large evolutionary context. Integrating additional species and families to the research on this topic can only advance our understanding of flower development and its evolution.In this chapter, we review the contribution that the Solanaceae family has made to the comprehension of flower development. While many of the general features of flower development (i.e., the key molecular players involved in flower meristem identity, inflorescence architecture or floral organ development) are similar to Arabidopsis, our main objective in this chapter is to highlight the points of divergence and emphasize specificities of the Solanaceae. We will not discuss the large topics of flowering time regulation, inflorescence architecture and fruit development, and we will restrict ourselves to the mechanisms included in a time window after the floral transition and before the fertilization. Moreover, this review will not be exhaustive of the large amount of work carried on the topic, and the choices that we made to describe in large details some stories from the literature are based on the soundness of the functional work performed, and surely as well on our own preferences and expertise.First, we will give a brief overview of the Solanaceae family and some of its specificities. Then, our focus will be on the molecular mechanisms controlling floral organ identity, for which extended functional work in petunia led to substantial revisions to the famous ABC model. Finally, after reviewing some studies on floral organ initiation and growth, we will discuss floral organ maturation, using the examples of the inflated calyx of the Chinese lantern Physalis and petunia petal pigmentation