Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1365-7) contains supplementary material, which is available to authorized users.

Comprehensive Proteomic Analysis of Lysine Ubiquitination in Seedling Leaves of Nicotiana tabacum

“…has been reported. 6 , 16 , 25 − 28 In this study, we analyzed the global lysine ubiquitylome of N. tabacum , which is a widely used model plant in molecular research. To identify K ub peptides in tobacco, LC–MS/MS along with highly specific enrichment analysis was used ( Figure 1 ).…”

“… 24 As one of the most valuable research biomaterials, common tobacco is widely used in the study of various aspects of botany, including genetic, cytological, physiological, and phytopathological studies. Because lysine ubiquitination has been well studied in the regulation of cellular and physiological processes in plants, animals, and humans in the past three decades, 25 elucidation of the ubiquitination sites in tobacco may provide an important breakthrough for understanding the potential role of this PTM in virus resistance in plants. In the present research, for the first time, we performed a comprehensive proteomic analysis of lysine-ubiquitinated (K ub ) sites in N. tabacum seedlings using high-resolution liquid chromatography-tandem mass spectrometry (LC–MS/MS) accompanied by highly sensitive immune-affinity purification and heuristic bioinformatics tools.…”

Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination

“…Then, each candidate soybean UBC sequence used as a query against the Pfam database to confirm its membership in the UBC family ( Finn et al., 2016 ). Repeat sequences were removed manually ( Zhang et al., 2018 ; Li et al., 2019 ). These predicted proteins exhibited significant diversity with respect to their predicted Mw, p I, and sequences ( Supplementary Table S1 ).…”

“…Compared with other groups, only group IX does not contain AtUBC. Interestingly, the 11 GmUBC genes chosen here were absent from the paper (Zhang et al, 2018) in which transcript for 50 UBC genes were detected in at least one of the 14 soybean plant tissues examined using the Soybase data. Therefore, we chose group IX as the research object.…”

“…In soybean, sequence analysis eventually determined 91 genes encoding typical UBC domain-containing proteins. The phylogenetic analysis indicated that, of the 91 genes, 71 encode ubiquitin E2 proteins, 11 encode UEV proteins, two encode RUB E2 proteins (RCE), four encode putative SUMO E2, one encodes ELC and two encode UFC1 E2 proteins (Zhang et al, 2018). Expression of AtUBC2 is capable of complementing the UV sensitivity of mutant rad6 (a E2-like protein) yeast (Zwirn et al, 1997).…”