Abstract
More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.
Highlights
To cite this version: Intikhab Alam, Yan-Qing Yang, Yong Wang, Mei-Lan Zhu, Heng-Bo Wang, et al
Finger proteins in B. rapa, two search strategies were used in the current study: first, we used the previous 469 RING proteins from A. thaliana[14] as BLASTp queries to perform multiple searches against the latest whole predicted proteome of B. rapa; second, each type of representative A. thaliana RING domain was used as a query to BLASTp against the same database of B. rapa genome
According to the amino acid residues at eight metal ligand positions and the distance between them, and taking into account the classification of the corresponding ortholog in A. thaliana as well as the phylogenetic analysis result of this study for those with one of the eight metal ligands modified, the 731 RING domains from 715 RING proteins were classified into eight RING types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1)
Summary
To cite this version: Intikhab Alam, Yan-Qing Yang, Yong Wang, Mei-Lan Zhu, Heng-Bo Wang, et al. The ubiquitination includes three steps: (1) Ub is activated in an ATP-depend interaction by the Ub-activating enzyme E1 to form an E1-Ub thioester linked intermediate; (2) the activated Ub is transferred to the Ub-conjugating enzyme E2 by interaction of E1-Ub with E2 to form a thioester linked E2-Ub intermediate; (3) Ub is attached, by covalence, to the substrate protein by the Ub-ligase enzyme E3, which interacts with both the E2-Ub and the target protein The repetition of these three steps attaches multiple Ub molecules to the substrate, which are thereafter recognized and degraded by the 26S proteasome, while the Ub molecules are recycled by the same pathway. There are two members of E1, 37 predicted members of E2, and more than 1400 predicted E3 Ub-ligases which constitute a large and diverse group and are mainly responsible for the substrate specificity[2,3]
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