title: The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis.
abstract: The covalent attachment of ubiquitin is an important determinant for selective protein degradation by the 26S proteasome in plants and animals. The specificity of ubiquitination is often controlled by ubiquitin-protein ligases (or E3s), which facilitate the transfer of ubiquitin to appropriate targets. One ligase type, the SCF E3s are composed of four proteins, cullin1/Cdc53, Rbx1/Roc1/Hrt1, Skp1, and an F-box protein. The F-box protein, which identifies the targets, binds to the Skp1 component of the complex through a degenerate N-terminal approximately 60-aa motif called the F-box. Using published F-boxes as queries, we have identified 694 potential F-box genes in Arabidopsis, making this gene superfamily one of the largest currently known in plants. Most of the encoded proteins contain interaction domains C-terminal to the F-box that presumably participate in substrate recognition. The F-box proteins can be classified via a phylogenetic approach into five major families, which can be further organized into multiple subfamilies. Sequence diversity within the subfamilies suggests that many F-box proteins have distinct functions and/or substrates. Representatives of all of the major families interact in yeast two-hybrid experiments with members of the Arabidopsis Skp family supporting their classification as F-box proteins. For some, a limited preference for Skps was observed, suggesting that a hierarchical organization of SCF complexes exists defined by distinct Skp/F-box protein pairs. Collectively, the data shows that Arabidopsis has exploited the SCF complex and the ubiquitin/26S proteasome pathway as a major route for cellular regulation and that a diverse array of SCF targets is likely present in plants.
authors.affiliation: Cellular and Molecular Biology Program and the Department of Horticulture, 1575 Linden Drive, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Gagne
authors.forename: Brian P
authors.initials: BP
authors.lastname: Downes
authors.forename: Shin-Han
authors.initials: SH
authors.lastname: Shiu
authors.forename: Adam M
authors.initials: AM
authors.lastname: Durski
authors.forename: Richard D
authors.initials: RD
authors.lastname: Vierstra
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant; D008025:Ligases / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D010453:Peptide Synthases / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D021122:Protein Subunits; D044843:SKP Cullin F-Box Protein Ligases; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D044767:Ubiquitin-Protein Ligases
chemical_list: D010940:Plant Proteins; D021122:Protein Subunits; D044843:SKP Cullin F-Box Protein Ligases; D044767:Ubiquitin-Protein Ligases; D008025:Ligases; D010453:Peptide Synthases