Plant Physiology Preview
Published on February 9, 2007; 10.1104/pp.106.091900
OPEN ACCESS ARTICLE
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.
This article has been cited by other articles:
|
|
|
|
 
S. Vyroubalova, K. Vaclavikova, V. Tureckova, O. Novak, M. Smehilova, T. Hluska, L. Ohnoutkova, I. Frebort, and P. Galuszka
Characterization of New Maize Genes Putatively Involved in Cytokinin Metabolism and Their Expression during Osmotic Stress in Relation to Cytokinin Levels
Plant Physiology,
September 1, 2009;
151(1):
433 - 447.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S.-Y. Jiang, A. Christoffels, R. Ramamoorthy, and S. Ramachandran
Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
Plant Physiology,
August 1, 2009;
150(4):
1997 - 2008.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
X. Wang, H. Tang, J. E. Bowers, and A. H. Paterson
Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
Genome Res.,
June 1, 2009;
19(6):
1026 - 1032.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
X. Hou, K. Xie, J. Yao, Z. Qi, and L. Xiong
A homolog of human ski-interacting protein in rice positively regulates cell viability and stress tolerance
PNAS,
April 14, 2009;
106(15):
6410 - 6415.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Gilkerson, J. Hu, J. Brown, A. Jones, T.-p. Sun, and J. Callis
Isolation and Characterization of cul1-7, a Recessive Allele of CULLIN1 That Disrupts SCF Function at the C Terminus of CUL1 in Arabidopsis thaliana
Genetics,
March 1, 2009;
181(3):
945 - 963.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Huang, N. L. Taylor, R. Narsai, H. Eubel, J. Whelan, and A. H. Millar
Experimental Analysis of the Rice Mitochondrial Proteome, Its Biogenesis, and Heterogeneity
Plant Physiology,
February 1, 2009;
149(2):
719 - 734.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. A. Howell, R. Narsai, A. Carroll, A. Ivanova, M. Lohse, B. Usadel, A. H. Millar, and J. Whelan
Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process
Plant Physiology,
February 1, 2009;
149(2):
961 - 980.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. Xu, H. Ma, M. Nei, and H. Kong
Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification
PNAS,
January 20, 2009;
106(3):
835 - 840.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. S.S. Ammiraju, F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A. C. Pontaroli, T. Rambo, J. Currie, K. Collura, et al.
Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set
PLANT CELL,
December 1, 2008;
20(12):
3191 - 3209.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P.-J. Cao, L. E. Bartley, K.-H. Jung, and P. C. Ronald
Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases
Mol Plant,
September 1, 2008;
1(5):
858 - 877.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H.-H. Liu, X. Tian, Y.-J. Li, C.-A. Wu, and C.-C. Zheng
Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana
RNA,
May 1, 2008;
14(5):
836 - 843.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. A. van den Burg, D. I. Tsitsigiannis, O. Rowland, J. Lo, G. Rallapalli, D. MacLean, F. L.W. Takken, and J. D.G. Jones
The F-Box Protein ACRE189/ACIF1 Regulates Cell Death and Defense Responses Activated during Pathogen Recognition in Tobacco and Tomato
PLANT CELL,
March 1, 2008;
20(3):
697 - 719.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Nijhawan, M. Jain, A. K. Tyagi, and J. P. Khurana
Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in Rice
Plant Physiology,
February 1, 2008;
146(2):
333 - 350.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
D. J. Gingerich, K. Hanada, S.-H. Shiu, and R. D. Vierstra
Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice
PLANT CELL,
August 1, 2007;
19(8):
2329 - 2348.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
