Adding precision tools to the plant biologists' toolbox with chemical genomics.

The scope of our knowledge regarding plant genetic mechanisms and gene functions is rapidly evolving and expanding. This is primarily due to the availability of genetic and genomic methods for investigating model species, such as Arabidopsis (Arabidopsis thaliana). To fuel future advances, current gene-based methods must be complemented by innovative interdisciplinary approaches that are broadly applicable to dynamic and complex biological processes and functional genomics analyses. We believe that the use of diverse chemicals to interrogate molecular processes provides a novel avenue for the rapid and effective dissection of biological mechanisms and gene networks in ways not feasible with mutation-based approaches. By facilitating the identification of new pathways and networks, this powerful technology, called chemical genomics, overcomes important gaps in ongoing functional genomics efforts in plants and allows for the eventual development of a framework for predictive modeling. The chemical genomics approach uses small molecules to modify or disrupt the functions of specific genes/proteins (Stockwell, 2000; Dobson, 2004; Lipinski and Hopkins, 2004), in contrast to classic genetics, in which mutations disrupt gene function. The underlying concept is that the functions of most proteins can be altered by the binding of a chemical, which can be found by screening large libraries for compounds that specifically affect a measurable process. There are four major aspects to chemical genomics: (1) library assembly/synthesis, or the creation of chemically diverse libraries of compounds; (2) screening, or the identification of compounds that affect a biological process of interest; (3) target identification, or the discovery of the protein targets of active compounds; and (4) target function and network discovery, or the use of the compounds to understand biological processes. It is usually necessary to screen a large number of compounds to find one or a few of sufficient specificity and efficacy to be useful, analogous to genetically screening for mutations causing a specific phenotype. However, the chemical genomics approach can address loss-of-function lethality and gene redundancy and allow instantaneous, reversible, tunable, and conditional control of a phenotype, providing many advantages over traditional genetic approaches. Well-characterized bioactive chemicals and their targets identified in Arabidopsis can be used in non-model species to improve agronomic traits and increase crop value. Bioactive chemicals have a long history of helping plant physiologists unravel mechanisms, including those involving inhibitors of GA biosynthesis, inhibitors of ethylene action, inhibitors of auxin transport, cytoskeleton-disrupting drugs, and inhibitors of GDPGTP exchange proteins, just to name a few. However, this approach has also met with strong criticism due to the complexities associated with understanding the action mode of compounds at the molecular level. This is one reason why drug companies must advertise the side effects of the drugs they sell. What has motivated biologists to revisit their interest in small molecules? While a little more than 10 million pure compounds are known in chemical literature, the potential chemical diversity (defined as the number of unique chemical structures) of compounds composed of carbon, hydrogen, nitrogen, oxygen, sulfur, phosphorous, and the halogens (the organic chemist’s periodic table) of molecular weight ,1,000 likely exceeds 10. The compounds that have thus far been tested for effects on plants are therefore only a minute fraction of the structural possibilities. The development of combinatorial and automated techniques for synthesizing novel compounds brought forth significant enhancement in the productivity of chemists and makes the likelihood of synthesizing molecular libraries that are representative of ‘‘chemical space’’ much greater. These advances in technology allow a systematic analysis of these chemicals. A more systematic approach means that we discover chemicals that specifically disrupt a process or the function of a protein. Once these chemicals are identified, we can combine their use with genetic screens to identify genes involved in the same process. The use of unbiased libraries of diverse small molecules will allow plant biologists to discover numerous new bioactive molecules valuable for studying the function of uncharacterized plant genes. Importantly, when combined with Arabidopsis functional genomics, chemical genomics is powerful for the effective and efficient analysis of regulatory networks underlying a specific process. Chemical genomics technologies have been used by industry for a long time. The only academic institutions devoted to this approach with a focus on * Corresponding author; e-mail [email protected]; fax 951–827– 2155. www.plantphysiol.org/cgi/doi/10.1104/pp.104.900155.