A complex systems approach to Arabidopsis root stem-cell niche developmental mechanisms: from molecules, to networks, to
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REVIEW
A complex systems approach to Arabidopsis root stem-cell niche developmental mechanisms: from molecules, to networks, to morphogenesis Eugenio Azpeitia • Elena R. Alvarez-Buylla
Received: 5 June 2012 / Accepted: 15 August 2012 Springer Science+Business Media B.V. 2012
Abstract Recent reports have shown that the molecular mechanisms involved in root stem-cell niche development in Arabidopsis thaliana are complex and contain several feedback loops and non-additive interactions that need to be analyzed using computational and formal approaches. Complex systems cannot be understood in terms of the behavior of their isolated components, but they emerge as a consequence of largely non-linear interactions among their components. The study of complex systems has provided a useful approach for the exploration of system-level characteristics and behaviors of the molecular networks involved in cell differentiation and morphogenesis during development. We analyzed the complex molecular networks underlying stem-cell niche patterning in the A. thaliana root in terms of some of the key dynamic traits of complex systems: self-organization, modularity and structural properties. We use these analyses to integrate the available root stem-cell niche molecular mechanisms data and postulate novel hypotheses, missing components and interactions and explain apparent contradictions in the literature. Keywords Root stem-cell niche Arabidopsis thaliana Gene regulatory networks Complex systems Self-organization Modularity
E. Azpeitia E. R. Alvarez-Buylla (&) Laboratorio de Gene´tica Molecular, Desarrollo y Evolucio´n de Plantas, Instituto de Ecologı´a, Centro de Ciencias de la Complejidad (C3), Universidad Nacional Auto´noma de Me´xico, Ciudad Universitaria, 04510 Coyoaca´n, Mexico, D.F., Mexico e-mail: [email protected]
Introduction Located at the tip of the root, the root stem-cell niche (RSCN) sustains the development and growth of all belowground tissues. Given its anatomical simplicity and accessibility, the Arabidopsis thaliana RSCN has become an excellent model system. The RSCN has been amenable to cellular and molecular genetic analyses unraveling a plethora of molecular regulatory mechanisms (MRMs) involved in maintaining its pattern and functionality. Partially due to the lack of data, until recently, most of the RSCN MRMs were understood as fragmented and isolated processes that were many times assumed to exhibit a linear relationship between genotype and phenotype. For example, currently, the identity and location of the RSCN is explained by the intersection of the expression patterns of a small set of transcription factors (Aida et al. 2004). However, recent findings reveal that a complex network composed of many interacting elements underlie RSCN patterning. In her great introductory book to complexity, Mitchell (2009) described a complex system as ‘‘…a system that exhibits nontrivial emergent and self-organizing behaviors’’. Indeed, complex systems comprise feedback loops and other non-linear interact
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