Blanc SVSE 6 - Sciences de la vie, de la santé et des écosystèmes : Génomique, génomique fonctionnelle, bioinformatique, biologie systémique

From gene regulatory networks to organ shape: an interdisciplinary study of leaf development. – MorphoLeaf

From gene regulatory networks to organ shape: an interdisciplinary study of leaf development

The goal of this project that brings together the complementary expertise of plant biologists, physicists and computer scientists is to elucidate how gene networks and hormone signalling are translated into specific growth patterns and generate shape taking as a model the leaf margin of plants.

The leaf margin, a model to understand how biological shapes are generated

Leaves can show diverse levels of dissections ranging from no (entire margin), mild (serration) to strong (lobes) incisions. The leaf itself can be either simple or dissected into units called leaflets. We have identified an evolutionary-conserved genetic factor the CUC genes that are required for the dissection of the leaf margin. The CUC genes are part of a network involving negative regulation by a miRNA, miR164 and possible response of the signalling molecule auxin. However, the interplay between the three actors of this network (CUC, miR164 and auxin) is not understood yet. Nor are known the cellular effects of the expression of the CUC genes and their link with differential growth of the leaf margin leading to serration. <br /> <br />This project brings together three partners that have complementary expertises in biology, image analysis and modelling to provide new insights into the mechanisms of leaf margin development. By combining biological observations and manipulations, quantitative measurements and modelling, we will specifically determine the dynamics of CUC/miR164A/auxin activities during leaf development and their interrelations, establish the contributions of cell proliferation and cell expansion to leaf serration and leaf shape and address the contribution of auxin and CUC2 to differential growth and hence to leaf serration and leaf shape. We will, stepwise, build, test and validate a model of leaf margin development integrating a regulatory network, cellular behaviour and morphogenesis. <br /> <br />

In this project, we will study leaf development at three different levels: the whole organ, cells, and genes / molecules. Specific methods for the extraction, quantification and modeling of biological data are developed in this project.
- At the level of the whole organ, we develop a method to automatically extract the outline of leaves at different stages of development and to identify automatically remarkable points such as tips and sinus of the teeth of the leaf margin. Methods are being developed to extract relevant quantitative data.

- At the genetic and molecular level, we will use different fluorescent reporter of different colors to monitor the transcriptional or translational activity of our genes of interest and the activity of auxin. In parallel, we formalize this network by a set of ordinary differential equations representing the dynamics of transcription and protein concentrations of CUC2, CUC3 and miR164, with auxin signaling as an imput of the network.
- Methods of analysis of the cellular level will be defined based on observations made on the two other levels

Morphological analysis and modeling:

More than 2,500 developing leaves (covering various genotypes, ranks or growing conditions) haven been sampled and digitalised. A method for the semi-automatic extraction of the contour of the leaves was developed. Several methods of automatic recognition of landmarks are being evaluated. By the end of 2012, we should produce a comprehensive method for the analysis of the leaf morphology (associated with a software) and use it to analyze the biological material collected.

Molecular analyzes:
All the transgenic lines to monitor the transcriptional and / or translational activity of the genes of interest were made and validated. We are currently combining several reporters in the same plants.

Network modeling:
We have formalized the network and obtained a set of ordinary differential equations. To study this network, we combined two approaches: the numerical solution of the differential equations to determine the dynamics of the network, the analytical solution of equations to reveal the invariant points. The theoretical results are in agreement with the data.


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Oral communication :
Kiss A., Cortizo M., Biot E., Burguet J., Godin C., Laufs P., Boudaoud A. : Quantification de la morphodynamique des dents des feuilles d’Arabidopsis thaliana.7eme Symposium Morphométrie et Evolution des Formes, Lyon, 24-25 mai 2012

Development is a complex process by which a single zygotic cell progressively enlarges, divides and gives rise to contrasted tissues and organs with specialised cell types. These processes have to be coordinated both in time and in space. Molecular genetic approaches, mainly based on the identification and study of mutants, have provided major insights into the underlying mechanisms and revealed diverse regulators such as genes, hormones… Because of the number of actors identified and the complexity of their interactions, an intuitive prediction of the effects of the perturbations of one of them on the whole network is becoming more and more difficult. Therefore, complementary approaches including modelling are currently developed via collaborations between biologists and non-biologists such as computer scientists, mathematicians or physicists in a new emerging field: developmental systems biology. However, the path leading from molecular interactions to shape is still far from reach in any organism. We propose to lead such a path in the context of Arabidopsis leaf development.

The goal of this project is to apply a systems biology approach combining biological investigation and modelling on leaf margin development to elucidate how gene networks and hormone signalling are translated into specific growth patterns and generate complex shapes.

The leaf is the main photosynthetic organ of the plant and its margin can show diverse levels of dissections ranging from no (entire margin), mild (serration) to strong (lobes) incisions. The leaf itself can be either simple or dissected into units called leaflets. Partner 1 has identified an evolutionary-conserved genetic factor the CUC genes that are required for the dissection of the leaf margin. The CUC genes are part of a network involving negative regulation by a miRNA, miR164 and possible response of the signalling molecule auxin. However, the interplay between the three actors of this network (CUC, miR164 and auxin) is not understood yet. Nor are known the cellular effects of the expression of the CUC genes and their link with differential growth of the leaf margin leading to serration.

This project brings together three partners that have complementary expertises in biology, image analysis and modelling to provide new insights into the mechanisms of leaf margin development. By combining biological observations and manipulations, quantitative measurements and modelling, we will specifically determine the dynamics of CUC/miR164A/auxin activities during leaf development and their interrelations, establish the contributions of cell proliferation and cell expansion to leaf serration and leaf shape and address the contribution of auxin and CUC2 to differential growth and hence to leaf serration and leaf shape. We will, stepwise, build, test and validate a model of leaf margin development integrating a regulatory network, cellular behaviour and morphogenesis.



Project coordinator

Monsieur Patrick LAUFS (INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE VERSAILLES GRIGNON) – laufs@versailles.inra.fr

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

INRIA INSTITUT NATIONAL DE RECHERCHE EN INFORMATIQUE ET EN AUTOMATIQUE -(INRIA Centre Sophia-Antipolis)
IJPB INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE VERSAILLES GRIGNON
RDP CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE RHONE-AUVERGNE

Help of the ANR 424,038 euros
Beginning and duration of the scientific project: - 36 Months

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