title: 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.
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.
authors.affiliation: Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
authors.forename: Aashima
authors.initials: A
authors.lastname: Nijhawan
authors.forename: Rita
authors.initials: R
authors.lastname: Arora
authors.forename: Pinky
authors.initials: P
authors.lastname: Agarwal
authors.forename: Swatismita
authors.initials: S
authors.lastname: Ray
authors.forename: Pooja
authors.initials: P
authors.lastname: Sharma
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kapoor
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.forename: Jitendra P
authors.initials: JP
authors.lastname: Khurana
mesh_terms: D002874:Chromosome Mapping; D044783:F-Box Proteins / Q000145:classification / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000502:physiology* / Q000528:radiation effects; D018745:Genome, Plant; D008027:Light; D012275:Oryza / Q000196:embryology / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012639:Seeds / Q000254:growth & development*
chemical_list: D044783:F-Box Proteins