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Published on February 9, 2007; 10.1104/pp.106.091900

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Received October 25, 2006
Accepted February 2, 2007

F-box Proteins in Rice. Genome-wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic Stress

Mukesh Jain , Aashima Nijhawan , Rita Arora , Pinky Agarwal , Swatismita Ray , Pooja Sharma , Sanjay Kapoor , Akhilesh K. Tyagi , and Jitendra P. Khurana *

Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110 021, India

* Corresponding author; email: khuranaj{at}genomeindia.org.

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (ca 40 amino acids). As components of the Skp1p-cullin-F-box (SCF) complex, F-box proteins are critical for the controlled degradation of cellular proteins. We have identified 687 potential F-box proteins in rice, the model monocotyledonous plant, by a reiterative database search. Computational analysis revealed the presence of several other functional domains, including leucine rich repeats (LRRs), kelch repeats, F-box associated domain (FBA), domain of unknown function (DUF) and tubby (TUB) in F-box proteins. Based upon their domain composition, they have been classified into ten subfamilies. Several putative novel conserved motifs have been identified in F-box proteins, which do not contain any other known functional domain. An analysis of a complete set of F-box proteins in rice is presented, including classification, chromosomal location, conserved motifs and phylogenetic relationship. It appears that the expansion of F-box family in rice, in large part, might have occurred due to localized gene duplications. Furthermore, comprehensive digital expression analysis of F-box protein encoding genes has been complemented with microarray analysis. The results reveal specific and/or overlapping expression of rice F-box protein encoding genes during floral transition as well as panicle and seed development. At least 43 F-box protein encoding genes have been found to be differentially expressed in rice seedlings subjected to different abiotic stress conditions. The expression of several F-box protein encoding genes is also influenced by light. The structure and function of F-box proteins in plants is discussed in light of these results and the published information. These data will be useful for prioritization of F-box proteins for functional validation in rice.




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