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,Rita Arora,Aashima Nijhawan,Pinky Agarwal,Akhilesh K Tyagi,Swatismita Ray,Pooja Sharma,Jitendra P Khurana,Sanjay Kapoor

doi:10.1104/pp.106.091900

Abstract

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (approximately 40 amino acids). As components of the Skp1p-cullin-F-box complex, F-box proteins are critical for the controlled degradation of cellular proteins. We have identified 687 potential F-box proteins in rice (Oryza sativa), the model monocotyledonous plant, by a reiterative database search. Computational analysis revealed the presence of several other functional domains, including leucine-rich repeats, kelch repeats, F-box associated domain, domain of unknown function, and tubby domain in F-box proteins. Based upon their domain composition, they have been classified into 10 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.

Highlights

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif
The C terminus of F-box proteins generally contains one or several highly variable proteinprotein interaction domains, for example, Leu-rich repeat (LRR), kelch repeat, tetratricopeptide repeat (TPR), and WD40 repeat that interact with specific targets
It has been demonstrated that many F-box proteins, including TIR1, which has been known for a long time to regulate the stability of Aux/ IAA proteins, act as auxin receptors in Arabidopsis (Gray et al, 2001; Dharmasiri et al, 2005a, 2005b; Kepinski and Leyser, 2005)

Summary

Introduction

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (approximately 40 amino acids). 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. The current availability of rice (Oryza sativa) genome sequence (International Rice Genome Sequencing Project, 2005) allows the identification of F-box protein-encoding genes in this monocotyledonous species and their comparative analysis with Arabidopsis, which will be useful in terms of studying the functional and evolutionary diversity of this superfamily in plants

Methods

Results

Conclusion