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GENOME ANALYSIS

Genome-Wide Identification of Arabidopsis Coiled-Coil Proteins and Establishment of the ARABI-COIL Database¹

Department of Plant Biology and Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, Ohio 43210 (A.R., I.M.); and Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, Ohio 43212 (S.M., S.J.S., M.A.M., E.A.S.)

Increasing evidence demonstrates the importance of long coiled-coil proteins for the spatial organization of cellular processes. Although several protein classes with long coiled-coil domains have been studied in animals and yeast, our knowledge about plant long coiled-coil proteins is very limited. The repeat nature of the coiled-coil sequence motif often prevents the simple identification of homologs of animal coiled-coil proteins by generic sequence similarity searches. As a consequence, counterparts of many animal proteins with long coiled-coil domains, like lamins, golgins, or microtubule organization center components, have not been identified yet in plants. Here, all Arabidopsis proteins predicted to contain long stretches of coiled-coil domains were identified by applying the algorithm MultiCoil to a genome-wide screen. A searchable protein database, ARABI-COIL (http://www.coiled-coil.org/arabidopsis), was established that integrates information on number, size, and position of predicted coiled-coil domains with subcellular localization signals, transmembrane domains, and available functional annotations. ARABI-COIL serves as a tool to sort and browse Arabidopsis long coiled-coil proteins to facilitate the identification and selection of candidate proteins of potential interest for specific research areas. Using the database, candidate proteins were identified for Arabidopsis membrane-bound, nuclear, and organellar long coiled-coil proteins.

¹ This work was supported by the National Science Foundation 2010 Project (grant no. NSF 0209339 to I.M.).

^* Corresponding author; e-mail meier.56{at}osu.edu; fax 614-292-5379.

Received November 5, 2003; returned for revision December 7, 2003; accepted December 19, 2003.

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