Forging Ahead on Arabidopsis

With completion of the genome sequence of the tiny mustard plant Arabidopsis imminent, researchers began anticipating the logical next step. Meeting in the fall of 1998 and again in January 2000 under the aegis of the National Science Foundation, they drew up a plan called the 2010 Project, which, if successful, would catalog the functions of all of 'the weed's' 25,000 or so genes. Their goal was ambitious: "to understand every molecular interaction in every cell throughout a plant life cycle."1 By doing so, they believed any scientist could construct "a virtual plant ... growing on a computer screen, stopping the process at any point in that development, and with the click of a mouse, access all the genetic information expressed in any organ or cell under a variety of environmental conditions." In other words, the group hoped to assemble over the next decade a complete instruction manual and parts description for how to build a plant from scratch. With The Scientists' report in hand, NSF was ready when molecular biologists completed the Arabidopsis genome in December 2000.2 The foundation made the 2010 Project a reality by soliciting proposals aimed at the plant's functional genomics. Says NSF director Rita Colwell, the agency's effort "is essential to this growing area of biotechnology research and its many applications." On Oct. 1, NSF announced Project 2010's first 28 awards totaling nearly $44 million. Selected from 106 competitive submissions, the awardees hale from 43 institutions and 20 states. According to Vicki Chandler, president of the American Society of Plant Biologists, "A better understanding [via the 2010 Project] of how plant genes function will have profound benefits for people throughout the world and for our environment. It's a new world we're entering." Daunting Task Deciphering the function of every gene in a multicellular organism such as Arabidopsis won't be easy. The task is particularly daunting in plants whose genomes contain large, multigene families characterized by nearly identical nucleotide sequences. According to awardee Alice Harmon of the University of Florida in Gainesville, "Plant researchers have a problem attacking multigene families-how do you figure out what an individual family member does? Are many [gene products] doing redundant, overlapping functions or individually important things?" The cytochrome P450 gene family is a good example. Mary Schuler of the University of Illinois in Urbana-Champaign wants to characterize Arabidopsis' P450 genes. That's quite a job-with 244 functional members, the plant P450 family is about four times larger than that of humans. Unfortunately, only about 20 of the members have defined functions. Organisms use cytochrome P450 enzymes to mitigate environmental insults such as toxic chemicals. The plant P450 library is large probably because, as immobile organisms, plants can't run away from many environmental threats the way animals do. They have to handle them. "Cytochrome P450s have representatives in many biochemical pathways," argues Schuler. "The diversity of the gene family has allowed plants to evolve pathways to deal with various predators. They're also involved in the synthesis of signal molecules," she adds. Schuler's group will try to place the products of various cytochrome P450 genes in biochemical pathways, and then study how those pathways are regulated by environmental stresses. She'll also visualize cells that respond to those stresses by hooking the promoter regions of P450 genes to reporter genes governing the synthesis of colored or fluorescent materials. "We're very excited about this funding opportunity for bringing functional genomics into the realm of plant cytochrome P450s," says Schuler. Signal Transduction, and More Harmon leads a national team of scientists trying to figure out what Arabidopsis' 34 calcium dependent protein kinases do. CDPKs, as they're called, together with four other closely related gene families, encode 88 kinase enzymes that attach phosphate groups to other proteins, thereby regulating their activity. Like the cytochrome P450s, protein kinases form crucial links in signal cascades that allow plants to respond to the environment. That's why they account for a hefty 9 percent of Arabidopsis' 125 million base pair genome. Harmon wants to identify the target of every kinase, thereby "identifying the signaling networks in which each member of the family participates." She hopes her team "can relate function to sequence," and in doing so, answer a question: "Do various branches of the kinase family tree have certain functions?" Magnus Nordborg of the University of Southern California in Los Angeles will mine the Arabidopsis genome for very different information. By assessing genetic differences between various Arabidopsis plants, Nordborg thinks he can piece together the species' genealogy. Rather than looking at the entire genome of one individual, he'll sequence 1,500-2,000 chromosomal segments consisting of 500-700 base pairs each from 96 carefully selected individuals. "The project represents the first serious attempt to describe genomic variation in a species," notes Nordborg in his grant abstract. That kind of information "doesn't exist in any other organism yet," he maintains. Nordborg's effort is analogous to the single nucleotide polymorphism, or SNP, database in humans, but the Arabidopsis study "will have more information than SNPs. Each fragment will contain several significant polymorphisms, plus insertions and deletions," he says. "It's much richer information than SNPS." The USC scientist is grateful for the NSF money, insisting he couldn't do the work without it. Nordborg isn't alone in using Project 2010 to investigate natural genetic variation in Arabidopsis. Alan Lloyd of the University of Texas in Austin leads a team of technicians, graduate students, and undergraduates, including students from nearby Austin Community College, mapping genetic polymorphisms in recombinant inbred lines, or RILs, derived from wild type accessions. According to his grant summary, Lloyd hopes to eventually "identify genes in local wild populations that are important for adaptation to many different environments and the result of many different evolutionary histories." A Large Portfolio Project 2010's other grants are equally diverse. Michael Sussman and Richard Amasino of the University of Wisconsin, Madison, will generate knockout mutations in all 25,000 genes. By analyzing changes in how the Arabidopsis plants develop and function, the ambitious researchers hope to identify gene function. Joseph Ecker of the Salk Institute for Biological Studies in La Jolla, Calif., will also catalog mutations-in this case, gene insertions. Gloria Coruzzi of Manhattan's New York University leads a team of scientists investigating genes that govern nitrogen uptake, metabolism, and allocation. Richard Trelease of Arizona State University in Tempe will sort out the function of peroxisomal membrane proteins. A complete list of 2010 Project awards, with links to grant summaries, is posted at www.nsf.gov/bio/pubs/awards/2010fy01.htm. Barry A. Palevitz (palevitz@dogwood.botany.uga.edu) is a contributing editor for The Scientist. References 1. J. Chory et al., "National Science Foundation sponsored workshop report: The 2010 Project. Functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them," Plant Physiology, 123:423-5, 2000. 2. B.A. Palevitz, "Arabidopsis genome. Completed project opens new doors for plant biologists," The Scientist, 15[1]:1, Jan. 8, 2001.

Forging Ahead on Arabidopsis

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