Arabidopsis thaliana as a model organism in systems biology

Abstract

Significant progress has been made in identification of genes and gene networks involved in key biological processes. Yet, how these genes and networks are coordinated over increasing levels of biological complexity, from cells to tissues to organs, remains unclear. To address complex biological questions, biologists are increasingly using high-throughput tools and systems biology approaches to examine complex biological systems at a global scale. A system is a network of interacting and interdependent components that shape the system's unique properties. Systems biology studies the organization of system components and their interactions, with the idea that unique properties of that system can be observed only through study of the system as a whole. The application of systems biology approaches to questions in plant biology has been informative. In this review, we give examples of how systems biology is currently being used in Arabidopsis to investigate the transcriptional networks regulating root development, the metabolic response to stress, and the genetic regulation of metabolic variability. From these studies, we are beginning obtain sufficient data to generate more accurate models for system function. Further investigation of plant systems will require data gathering from specific cells and tissues, continued improvement in metabolic technologies, and novel computational methods for data visualization and modeling.

Keywords: Root development; high-throughput methods; metabolism; quantitative traits; transcriptional networks.

Figure 1

Diagram of the Arabidopsis root tissues and longitudinal sections used in microarray expression profiles in Brady et al. Colors represent the different developmental stage and cell types examined (14 individual tissues). Thirteen longitudinal samples were analyzed and the red lines indicate their relative positions. Stem cells are located in section 1 and cells further from the stem cells are progressively more differentiated. The developmental zones are bracketed on the right. In the meristematic zone, stem cells undergo asymmetric divisions that recapitulate the stem cells and produce daughter cells, which will divide several more times within this zone. In the elongation zone, division ceases and the cells rapidly expand longitudinally. Finally, in the maturation zone, cells differentiate acquiring their specialized features. Note the radial symmetry particularly in the outer tissues of the root. From Brady, S.M., et al., A high-resolution root spatiotemporal map reveals dominant expression patterns. Science, 2007. 318(5851): p. 801–806. Reprinted with permission from AAAS.

Figure 2

Schmatic of a network showing interdependence of system components and response to feedback based on developmental or environmental cues. The metabolic profile of a cell or system provides a measure of the output of the genetic network but may also serve as an input. In response to external cues metabolites feed back into networks, ultimately altering behavior of the system. Figure adapted from Weckworth [23].

Figure 3

Natural variation in leaf growth and development in several Arabidopsis accessions collected from distinct geographical locations. Natural variation is often observed as a phenotypic continuum, as opposed to presence or absence of the trait. Here, for example, all accessions have leaves, but the size, shape, and number is variable. The molecular mechanisms regulating quantitative traits such as leaf size and shape can often be applied to improve crop science and plant breeding programs. Figure from the website of Dr. Matthieu Reymond, Max Planck Institute for Plant Breeding Research, used with permission of Dr. Martin Koornneef.