From Genes to Flower Patterns and Evolution: Dynamic Models of Gene Regulatory Networks |
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Authors: | Álvaro Chaos Max Aldana Carlos Espinosa-Soto Berenice García Ponce de León Adriana Garay Arroyo Elena R Alvarez-Buylla |
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Institution: | (1) Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Dpto. de Ecología Funcional, Instituto de Ecología, UNAM, C. P. 04510 México, DF, México;(2) Centro de Ciencias Físicas, UNAM, C. P. 62251, Apartado Postal 48-3, Cuernavaca Morelos, México |
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Abstract: | Genes and proteins form complex dynamical systems or gene regulatory networks (GRN) that can reach several steady states (attractors).
These may be associated with distinct cell types. In plants, the ABC combinatorial model establishes the necessary gene combinations
for floral organ cell specification. We have developed dynamic gene regulatory network (GRN) models to understand how the
combinatorial selection of gene activity is established during floral organ primordia specification as a result of the concerted
action of ABC and non-ABC genes. Our analyses have shown that the floral organ specification GRN reaches six attractors with
gene configurations observed in primordial cell types during early stages of flower development and four that correspond to
regions of the inflorescence meristem. This suggests that it is the overall GRN dynamics rather than precise signals that
underlie the ABC model. Furthermore, our analyses suggest that the steady states of the GRN are robust to random alterations
of the logical functions that define the gene interactions. Here we have updated the GRN model and have systematically altered
the outputs of all the logical functions and addressed in which cases the original attractors are recovered. We then reduced
the original three-state GRN to a two-state (Boolean) GRN and performed the same systematic perturbation analysis. Interestingly,
the Boolean GRN reaches the same number and type of attractors as reached by the three-state GRN, and it responds to perturbations
in a qualitatively identical manner as the original GRN. These results suggest that a Boolean model is sufficient to capture
the dynamical features of the floral network and provide additional support for the robustness of the floral GRN. These findings
further support that the GRN model provides a dynamical explanation for the ABC model and that the floral GRN robustness could
be behind the widespread conservation of the floral plan among eudicotyledoneous plants. Other aspects of evolution of flower
organ arrangement and ABC gene expression patterns are discussed in the context of the approach proposed here.
álvaro Chaos, Max Aldana and Elena Alvarez-Buylla contributed equally to this work. |
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Keywords: | Gene regulatory networks Flowers Pattern formation Dynamic models Discrete models Evolution Development Boolean networks Self-organization ABC model |
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