Abstract
Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.
Highlights
Biological and cellular processes in plants are regulated by several mechanisms, such as controlled gene expression, protein synthesis, protein modification, protein degradation, and interactions among molecules
The results of the present study provide novel information regarding the classification and expression of F-box proteins that may be useful for functional research on the different developmental stages of wheat
HMM profiling of the F-box proteins was conducted with the HMM files of F-box (PF00646), F-box-like (PF12937), F-box-like2 (PF13013), FBA1 (PF07734), FBA2 (PF07735), FBA3 (PF08268), and FBD (PF08387) domains, which were provided by Pfam [22] and searched against a protein database of the wheat genome using the HMMER3 tool with default parameters [23]
Summary
Biological and cellular processes in plants are regulated by several mechanisms, such as controlled gene expression, protein synthesis, protein modification, protein degradation, and interactions among molecules. The ubiquitin proteasome system (UPS), which selectively regulates protein degradation via the 26S proteasome, is a key mechanism for the post-translational control of several intracellular proteins. The UPS plays a significant role in the regulation of signal transduction, metabolic regulation, differentiation, cell cycle transition, and stress response by causing the degradation of specific proteins [1,2]. Several types of E3 ubiquitin ligases have been characterized by the presence of specific domains, including homology to the E6-AP C-terminus domain and a really interesting new gene/U-box domain, and Cullin–Ring ubiquitin ligase.
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