title: Classification and expression analysis of Arabidopsis F-box-containing protein genes.
abstract: F-box proteins regulate diverse cellular processes, including cell cycle transition, transcriptional regulation and signal transduction, by playing roles in Skp1p-cullin-F-box protein (SCF) complexes or non-SCF complexes. F-box proteins are encoded by a large gene family. Our database search revealed that at least 568 F-box protein genes are present in the Arabidopsis thaliana (Arabidopsis) genome. Domain search analysis using SMART and Pfam-A databases revealed that 67 of the F-box proteins contained Kelch repeats and 29 contained leucine-rich repeats (LRRs). Interestingly only two F-box proteins contained WD40 repeats that are found in many F-box proteins of other organisms. Kelch repeats, LRRs and WD40 repeats are implicated in protein-protein interactions. This analysis also resulted in the finding of several unique functional domains; however, 448 of the F-box proteins did not contain any known domains. Therefore, these proteins were used to search the Pfam-B database to find novel domains, and three putative ones were found. These domain search analyses led us to classify the Arabidopsis F-box proteins into at least 19 groups based on their domain structures. Macro array analysis showed that several F-box protein genes are expressed in a tissue-specific manner.
authors.affiliation: Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suyehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Kuroda
authors.forename: Naoki
authors.initials: N
authors.lastname: Takahashi
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Shimada
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Minami
authors.initials: M
authors.lastname: Matsui
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002453:Cell Cycle / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D000090263:Leucine-Rich Repeat Proteins; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D025941:Protein Interaction Mapping; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: C120363:ASK1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D002352:Carrier Proteins; D000090263:Leucine-Rich Repeat Proteins; D011506:Proteins; D014157:Transcription Factors