Minisymposium 7: Emerging Technologies
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M0701: The Virtual Plastid: Functional and Informatic Annotation of the Arabidopsis Plastid Proteome
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Presenter: |
Last, Robert Contact Presenter |
Authors | Last, Robert (A) (B) Lu, Yan (A) Savage, Linda (A) Benning, Christoph (A) DellaPenna, Dean (A) Ohlrogge, John (B) Osteryoung, Katherine (B) Shachar-Hill, Yair (B) Weber, Andreas (B) Wedemeyer, William (A) (C) Wilkerson, Curtis (D) | | Affiliations: |
(A): Department of Biochemistry and Molecular Biology, Michigan State University
(B): Department of Plant Biology, Michigan State University
(C): Department of Physics, Michigan State University
(D): Research Technology Support Facility, Michigan State University
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| Web Site: | http://www.bch.msu.edu/faculty/last.html | |
The plastid is an attractive target for a functional genomics approach in Arabidopsis because it has a large but manageable parts list of <4,500 proteins that are targeted to or synthesized within it. This relative simplicity suggests that the community will soon be able to measure the abundance of the transcripts, proteins and small molecules essential to plastid function, and from such data, build an integrative model of how these components function together. We must first connect individual genes to function via an array of functional genomic and direct biochemical assays, including measures of network-wide metabolic function.
This project uses several approaches to improve annotation for the nuclear genes predicted to encode plastid targeted proteins. Thousands of homozygous t-DNA insertion lines are being subjected to a dozen parallel phenotypic screens. These include plant and chloroplast morphology, chlorophyll fluorescence kinetics as well as analysis of a diverse set of metabolites that are synthesized in the plastid (lipids, starch, amino acids, tocopherols, and carotenoids). Two informatics approaches will be used to develop hypotheses regarding genes of unknown function, thus complementing the phenotypic screening. First, homology-based protein structural models will be developed for the inferred gene products. Second, the project will harness well documented genetic linkage between bacterial genes of related function (http://www.figresearch.com/) and ask whether bacterial homologues of Arabidopsis genes of unknown function are in close proximity to bacterial genes of documented function. The results of these laboratory and informatic analyses will be made available at the project website (www.plastid.msu.edu).
