PROTEOMICS PROJECTS
Researchers participating in the Arabidopsis 2010 Project initiated by the U.S. National Science Foundation (NSF) have a very ambitious goal: to determine the functions of all of the genes of the model plant Arabidopsis thaliana by the year 2010. To meet this challenge, several researchers are incorporating proteomics techniques into their studies in addition to genomics, transcriptomics, and classical genetics methods. “When the 2010 Project started in 2000, we didn’t get as many proposals that had a proteomics emphasis, but now I am seeing that it is becoming an integral part of these projects,” says Parag Chitnis of NSF. The idea for the 2010 Project grew out of meetings with plant researchers involved with the A. thaliana sequencing effort, which was called the Multinational Coordinated A. thaliana Genome Research Project. The sequencing was largely funded in the U.S. by NSF and was organized internationally by a group of representatives from participating countries. After the completion of the sequence in 2000, NSF consulted with the group about future directions for A. thaliana research. Everyone involved realized that “the obvious next step was to try to find out what all those genes do,” according to Chitnis. NSF acted on this idea by announcing the Arabidopsis 2010 Project with funding of $25 million per year for 10 years for U.S.-based research. Meanwhile, the close-knit A. thaliana community continued to meet and discuss directions for the field. In 2001, the group that NSF consulted with evolved into the Multinational Arabidopsis Steering Committee (MASC). They then started the Multinational Coordinated A. thaliana Functional Genomics Project to organize research worldwide on this topic. With this global venture, MASC ensures that efforts are not duplicated unnecessarily and that all important research topics are being addressed. Chitnis says that through MASC, NSF learned that the German government’s science funding agency, Deutsche For schungsgemeinschaft (DFG), also was funding functional genomics studies on A. thaliana. Officials from NSF and
DFG therefore decided to coordinate their efforts. NSF has an annual funding schedule for its program, whereas DFG has a 3-year cycle, so in those years when both agencies hold competitions, it becomes a joint affair. Every 3 years, therefore, German and U.S. proposals are evaluated by the same panel, which includes reviewers from both countries. This year’s joint competition encouraged collaborations among U.S. and German researchers. In addition, researchers were asked to address one of three emphasis areas: the use of genome-wide approaches to benchmark the genome, the development of tools SORINA POPESCU
Proteomics in the garden: the Arabidopsis 2010 Project
Plant proteomics. Researchers are using proteomics techniques, such as protein microarrays, to study the functions of A. thaliana genes.
and resources for the community, and the use of high-throughput methods and modeling to generate exemplary interaction networks. Over the years, the 2010 Project has funded 99 proposals, including renewals. Estimating the number of proteo mics projects, however, is a difficult task. Chitnis explains that several projects include a proteomics component, but few focus solely on proteomics. For example, a research team might use a proteomics method to identify a component of a complex but then determine the function of that component with knockout strains. Currently funded projects include those that address phosphoproteomics, organellar proteomics, proteomics technology development, protein–protein interac-
934 Journal of Proteome Research • Vol. 6, No. 3, 2007
tions, and protein localization. Proteomics also is on the minds of MASC researchers. Just last year, they set up a subcommittee on the topic with the goal of establishing strong interactions among Arabidopsis proteomics labs worldwide, according to Wolfram Weckwerth, who is chair of the subcommittee and is at the Max Planck Institute of Molecular Plant Physiology (Germany). The group plans to organize workshops to bring researchers together outside of the annual MASC meetings held at the International Arabidopsis Conference. “Another strong aim is to coordinate proteomics studies with the MASC bioinformatics subcommittee and the MASC metabolomics subcommittee in terms of database standards and combined protein, metabolite, and transcript profiling and phenotyping,” says Weckwerth. Although the A. thaliana functional genomics projects are progressing well in general, Weckwerth says that technical obstacles still must be overcome. “The development of proteomics techniques and their application to plant biology show strong progress, and some of them are probably groundbreaking methods that are generally applicable. However, proteomics has not yet reached the goal,” he says. “Here, we are still in the process of initial data generation, and in the face of the enormous complexity of the dynamic proteome, it will require further method development, especially in the fields of quantitative proteomics and signaling.” As the 2010 deadline looms, A. thaliana researchers already are looking ahead to the future. In fact, an Arabidopsis 2020 Project was recently proposed by North American plant researchers who convened in 2005 to assess the progress of the 2010 Project. In their workshop report, they state that the next project could include studies on the variations of genes and cellular networks over time and between populations and A. thaliana species. Chitnis says NSF is open to the idea. “The Arabidopsis 2010 Project started through a series of workshops that developed the idea. Similarly, now there could be workshops to develop the idea of what happens after 2010,” he says. —Katie Cottingham
