Abstract
BackgroundUbiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. The ubiquitination process typically involves three distinct classes of enzymes, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3). To date, a comprehensive identification and analysis of core components comprising of the whole soybean (Glycine max) ubiquitin system (UBS) has not been reported.ResultsWe performed a systematic, genome-wide analysis of genes that encode core members of the soybean UBS in this study. A total of 1431 genes were identified with high confidence to encode putative soybean UBS components, including 4 genes encoding E1s, 71 genes that encode the E2s, and 1356 genes encoding the E3-related components. Among the E3-encoding genes, 760 encode RING-type E3s, 124 encode U-box domain-containing E3s, and 472 encode F-box proteins. To find out whether the identified soybean UBS genes encode active enzymes, a set of genes were randomly selected and the enzymatic activities of their recombinant proteins were tested. Thioester assays indicated proteins encoded by the soybean E1 gene GmUBA1 and the majority of selected E2 genes are active E1 or E2 enzymes, respectively. Meanwhile, most of the purified RING and U-box domain-containing proteins displayed E3 activity in the in vitro ubiquitination assay. In addition, 1034 of the identified soybean UBS genes were found to express in at least one of 14 soybean tissues examined and the transcript level of 338 soybean USB genes were significantly changed after abiotic or biotic (Fusarium oxysporum and Rhizobium strains) stress treatment. Finally, the expression level of a large number of the identified soybean UBS-related genes was found significantly altered after soybean cyst nematode (SCN) treatment, suggesting the soybean UBS potentially plays an important role in soybean immunity against SCN.ConclusionsOur findings indicate the presence of a large and diverse number of core UBS proteins in the soybean genome, which suggests that target-specific modification by ubiquitin is a complex and important part of cellular and physiological regulation in soybean. We also revealed certain members of the soybean UBS may be involved in immunity against soybean cyst nematode (SCN). This study sets up an essential foundation for further functional characterization of the soybean UBS in various physiological processes, such as host immunity against SCN.
Highlights
Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes
Our findings indicate the presence of a large and diverse number of core ubiquitin system (UBS) proteins in the soybean genome, which suggests that target-specific modification by ubiquitin is a complex and important part of cellular and physiological regulation in soybean
We revealed certain members of the soybean UBS may be involved in immunity against soybean cyst nematode (SCN)
Summary
Ubiquitination is a major post-translational protein modification that regulates essentially all cellular and physiological pathways in eukaryotes. Ubiquitination is a major post-translational protein modification that plays an important role in many cellular and physiological processes in eukaryotes [1]. It involves covalently attaching ubiquitin, a highly conserved small protein, to substrate through sequential reactions that are catalyzed by three classes of enzymes: ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3) [2]. The E1 enzyme first activates free ubiquitin in presence of ATP hydrolysis, leading to the formation of a thioester-linkage in which the C-terminal glycine of the ubiquitin molecule is linked with the cysteine residue at the active center of E1. The enzymatic cascade can be repeated after the first ubiquitin is attached to the substrate protein, resulting in a polymeric ubiquitin chain being linked to the substrate protein where the linkage between ubiquitin moieties determines the substrate’s fate in the cell [3]
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