Update on Cell Wall Navigator Database The Cell Wall Navigator Database . A Systems-Based Approach to Organism-Unrestricted Mining of Protein Families Involved in Cell Wall Metabolism 1

Despite the importance of cell walls to the biology of plants, not much is known about the biosynthesis and function of their major macromolecular components. From the known complexity of the cell wall structure, we can predict that its synthesis requires hundreds of enzymes, but biochemical approaches have been unsuccessful thus far in characterizing more than a few of them (Henrissat et al., 2001; Reiter, 2002; Vincken et al., 2003). Likewise, many proteins involved in cell wall reorganization, degradation, and the signaling pathways that control cell wall metabolism remain functionally uncharacterized. Comparative molecular genetic studies have not been useful because the walls of other organism groups, such as bacteria and yeast, are fundamentally different in composition, structure, and function from those of plants. In addition, the wide evolutionary distances between the kingdoms create serious limitations for sequence similaritybased approaches. Recent advances in genomics make it possible to identify quickly large numbers of genes as being putatively involved in particular plant cell processes. These new resources provide unexplored opportunities for integrative systems biology studies. In addition, the availability of plant genome sequences and large expressed sequence tag (EST) sets from cell wall model species, like cotton (Gossypium sp.) and poplar (Populus sp.), are excellent tools for comparative studies. However, with the new resources for identifying candidate genes encoding biosynthetic enzymes and regulatory proteins comes the challenge of extracting the critical information from complex data sets to guide the functional analysis of these genes and the proteins they encode. Many Web services are available for individual cell wall-related protein families, primarily from Arabidopsis. Yet, efforts to consolidate the knowledge concerning the different enzyme and structural protein families for a wide spectrum of plant and non-plant species in one interface are missing. Our objective is to fill this gap by creating and maintaining Cell Wall Navigator (CWN; http://bioinfo.ucr.edu/projects/Cellwall/index.pl), a Web-based database that integrates cell wall-related protein families and allows easy comparison among sequences derived from fully sequenced plant genomes plus the known protein sequences from other species. Databases with global family cluster information for all known proteins are available (Krause et al., 2002), but their interfaces typically lack the flexibility required for process-oriented databases (Tchieu et al., 2003), which are more suited for organizing detailed functional and annotation information. The unique features of the CWN database are (1) its adaptable design for organizing complex protein families across many organisms to cover the complete space of known sequences, (2) its flexible architecture for rapid integration of new families, (3) its automated update and analysis pipeline to maintain current information, and (4) its numerous visualization and interactive mining tools.