Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database.
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.
Rose
Annkatrin
A
Department of Plant Biology and Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, Ohio 43210, USA.
Manikantan
Sankaraganesh
S
Schraegle
Shannon J
SJ
Maloy
Michael A
MA
Stahlberg
Eric A
EA
Meier
Iris
I
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics*; D002451:Cell Compartmentation; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D018745:Genome, Plant; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary
D029681:Arabidopsis Proteins; D008565:Membrane Proteins; D009687:Nuclear Proteins