Dr. Annkatrin Rose

Computational identification of plant nuclear envelope and Golgi coiled-coil proteins

Annkatrin Rose
Appalachian State University, Boone, NC 28608, USA

Long coiled-coil proteins such as lamins and golgins play an important role in the organization of the nuclear envelope and Golgi apparatus in animal cells. However, many of these long coiled-coil proteins do not appear to have homologues in plant cells. The repeat nature of the coiled-coil sequence motif often renders sequence similarity searches inconclusive, but on the other hand facilitates the computational prediction of protein domains capable of forming coiled-coil structures. Using the algorithm MultiCoil on the Arabidopsis and rice genomes, we identified plant proteins predicted to contain long coiled-coil domains. When combined with the prediction of subcellular localization signals and transmembrane domains, this plant coiled-coil database allows for the identification of putative membrane-bound, nuclear, and organellar long coiled-coil proteins. We found twenty putative nuclear and four putative Golgi long coiled-coil proteins encoded by the Arabidopsis genome. Nuclear proteins include the nuclear pore protein NUA1, proteins similar to the nuclear envelope-localized NMCP1 from carrot, and a protein interacting with RanGAP1, a component of the Ran cycle that shows nuclear envelope localization in plant cells. The group of putative golgins included the golgin CASP. Taken together, these results demonstrate the usefulness of computational tools for the identification of candidate nuclear envelope and Golgi proteins in plant cells.

Invited talk at the SEB Satellite Meeting - Nuclear Envelope and Golgi, Marseille, France, July 6-10, 2008.