Abstract
U-box E3 ligase genes play specific roles in protein degradation by post-translational modification in plant signaling pathways, developmental stages, and stress responses; however, little is known about U-box E3 genes in wheat. We identified 213 U-box E3 genes in wheat based on U-box and other functional domains in their genome sequences. The U-box E3 genes were distributed among 21 chromosomes and most showed high sequence homology with homoeologous U-box E3 genes. Synteny analysis of wheat U-box E3 genes was conducted with other plant species such as Brachypodium distachyon, barley, rice, Triricum uratu, and Aegilops tauschii. A total of 209 RNA-seq samples representing 22 tissue types, from grain, root, leaf, and spike samples across multiple time points, were analyzed for clustering of U-box E3 gene expression during developmental stages, and the genes responded differently in various tissues and developmental stages. In addition, expression analysis of U-box E3 genes under abiotic stress, including drought, heat, and both heat and drought, and cold conditions, was conducted to provide information on U-box E3 gene expression under specific stress conditions. This analysis of U-box E3 genes could provide valuable information to elucidate biological functions for a better understanding of U-box E3 genes in wheat.
Highlights
Accepted: 3 March 2021The ubiquitin–proteasome system (UPS), which regulates selective protein degradation via the 26S proteasome, is one of the major mechanisms for post-translational regulation of gene expression and protein quality control in eukaryotes
A total of 213 putative U-box E3 genes were identified by hidden Markov model (HMM) profiling against the local protein database of the IWGSC (International Wheat Genome Sequencing Consortium)
E3 ubiquitin ligase is the largest family of enzymes that catalyze the covalent attachment of a small protein modifier, ubiquitin, to substrates in eukaryotic cells, causing ubiquitin proteasomal degradation [24]
Summary
The ubiquitin–proteasome system (UPS), which regulates selective protein degradation via the 26S proteasome, is one of the major mechanisms for post-translational regulation of gene expression and protein quality control in eukaryotes. 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]. The UPS involves a cascade of three steps: ATP-dependent activation of ubiquitin by a ubiquitin-activating enzyme (E1), transfer of ubiquitin to a conjugating enzyme (E2), and conveyance of ubiquitin to a substrate protein by E3 [3]. The E3 ubiquitin ligases are the largest family among all three enzymes and are classified into different families based on their structure, function, and substrate specificity. New Gene (RING)/U-box E3 domain, and Cullin-RING ubiquitin ligase.
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