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Plant and Cell Physiology, 2002, Vol. 43, No. 10 1073-1085
© 2002 Oxford University Press

Classification and Expression Analysis of Arabidopsis F-Box-Containing Protein Genes

Hirofumi Kuroda1, Naoki Takahashi1,2, Hiroaki Shimada2, Motoaki Seki3,4, Kazuo Shinozaki3,4 and Minami Matsui1,5

1 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
2 Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan
3 Plant Mutation 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
4 Plant Molecular Biology Laboratory, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan

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.

5 Corresponding author: E-mail, minami@postman.riken.go.jp; Fax, +81-45-503-9586.


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