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Toward a Systems Approach to Understanding Plant Cell Walls
Chris Somerville,1,2* Stefan Bauer,1 Ginger Brininstool,1 Michelle Facette,1,2 Thorsten Hamann,1 Jennifer Milne,1 Erin Osborne,1 Alex Paredez,1,2 Staffan Persson,1 Ted Raab,1 Sonja Vorwerk,1 Heather Youngs1,2 Cell walls also provide a barrier to infection by pathogens. Exogenous application of cell wall fragments to uninfectedplants triggers defensive reactions, indicating the existence of glycan-activated signal transduction chains. It has been proposed that some of the structural complexity in plant cell wall composition reflects the presence of latent signal molecules, which trigger defensive responses when they are released during the cell wall degradation that accompanies pathogenesis (12). Several lines ofevidence have also implicated cell wall polysaccharide fragments and proteoglycans in developmental processes (13–15). For example, deglycosylation inactivated a proteoglycan named xylogen that mediates intercellular interactions required for xylem differentiation in cultured Zinnia cells (14). Thus, the design principles of cell walls cannot be understood solely in the context of mechanical properties.One of the defining features of plants is a body plan based on the physical properties of cell walls. Structural analyses of the polysaccharide components, combined with highresolution imaging, have provided the basis for much of the current understanding of cell walls. The application of genetic methods has begun to provide new insights into how walls are made, how they are controlled, and howthey function. However, progress in integrating biophysical, developmental, and genetic information into a useful model will require a system-based approach.

lant cell walls are complex and dynamic structures composed mostly of polysaccharides with high molecular weights (1–4), highly glycosylated proteins, and lignin. As a measure of the complexity, the Arabidopsis genome contains more than 730genes encoding putative glycosyltransferases or glycosyl hydrolases (5) and several hundred additional genes encoding other types of proteins implicated in wall biosynthesis or function. Although their general catalytic activity can often be inferred from sequence, the precise enzymatic function and biological role of most of these proteins are unknown (2). For example, genetic analysis hasidentified the specific biological role for only two of the more than 170 gene products with similarity to pectin-degrading enzymes (6, 7). Faced with the prospect of analyzing the function of 1000 or more genes that may contribute to the synthesis and remodeling of cell walls, we explored the idea that a systems approach may provide a useful framework for defining the hierarchy of essential questions.The concept of systems biology has recently emerged as a way of envisioning how multifactorial biological processes operate as a whole (8). The concept is usually applied to understanding networks of genes or gene products but is more broadly applicable. Kitano (8) defines four key elements in a system: the design principles, system structure, the control method, and the system dynamics. Here, weattempted to evaluate the current state of knowledge about the poly1 Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA. 2 Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.


saccharide components of dicotyledonous plant cell walls in the context of these elements. Not surprisingly, our analysis highlights many majorgaps in our knowledge. However, the application of genomics, molecular genetics, and new analytical methods should provide many opportunities to close some gaps in the foreseeable future.

Design Principles
The body plan of a higher plant is essentially like a building made of ‘‘osmotic bricks.’’ Each cell is osmotically pressurized to between 0.1 and 3.0 MPa (1 MPa È 145 pounds per square...