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, 7 (1), 13601

Comprehensive Profiling of Lysine Ubiquitome Reveals Diverse Functions of Lysine Ubiquitination in Common Wheat

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Comprehensive Profiling of Lysine Ubiquitome Reveals Diverse Functions of Lysine Ubiquitination in Common Wheat

Ning Zhang et al. Sci Rep.

Abstract

Protein ubiquitination, which is a major post-translational modifications that occurs in eukaryotic cells, is involved in diverse biological processes. To date, large-scale profiling of the ubiquitome in common wheat has not been reported, despite its status as the major cereal crop in the world. Here, we performed the first ubiquitome analysis of the common wheat (Triticum aestivum L.) variety, Aikang 58. Overall, 433 lysine modification sites were identified in 285 proteins in wheat seedlings, and four putative ubiquitination motifs were revealed. In particular, 83 of the 285 ubiquitinated proteins had ubiquitination orthologs in Oryza sativa L., and Arabidopsis thaliana. Ubiquitylated lysines were found to have a significantly different preference for secondary structures when compared with the all lysines. In accordance with previous studies, proteins related to binding and catalytic activity were predicted to be the preferential targets of lysine ubiquitination. Besides, protein interaction network analysis reveals that diverse interactions are modulated by protein ubiquitination. Bioinformatics analysis revealed that the ubiquitinated proteins were involved in diverse biological processes. Our data provides a global view of the ubiquitome in common wheat for the first time and lays a foundation for exploring the physiological role of lysine ubiquitination in wheat and other plants.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Overview of experimental procedures used in this study.
Figure 2
Figure 2
Proteome-wide identification of lysine ubiquitination sites in wheat. (A) Mass error distribution of all identified peptides. (B) Peptide length distribution. (C) Pie chart illustrating the number and percentage of lysine ubiquitination sites per protein.
Figure 3
Figure 3
Ubiquitinated lysine motifs in wheat. (A) Ubiquitination motifs and the conservation of ubiquitination sites. The height of each letter corresponding to the frequency of the amino acid residue in that position. The central K stands for the ubiquitinated lysine. (B) The number of identified ubiquitinated peptides in each motif.
Figure 4
Figure 4
(A) Probabilities of lysine ubiquitination in different protein secondary structures (alpha-helix, beta-strand and coli). (B) Predicted surface accessibility of ubiquitination sites. All lysine sites were in green and ubiquitinated lysine sites were in red.
Figure 5
Figure 5
Pie charts of the distribution of ubiquitinated proteins based on their predicted molecular functions (A), biological processes (B), cellular components (C), and metabolic pathways (D).
Figure 6
Figure 6
Ubiquitinated subunits of the 40S and 60S ribosome complexes in wheat. Ubiquitinated subunits are highlighted in red. Source: Kanehisa et al..
Figure 7
Figure 7
Ubiquitinated proteins in representative metabolic pathways in terms of carbon fixation in photosynthetic organisms in wheat. Ubiquitinated proteins are highlighted in red. W5HZ47, C1J959 and W5HA05 corresponds to 4.1.2.13, W5BG62 corresponds to 4.1.1.39, D8L9K9 corresponds to 3.1.3.11, and A0A096UTL2 corresponds to 1.2.1.12. Source: Kanehisa et al..
Figure 8
Figure 8
Interaction networks of the ubiquitinated proteins in wheat using String software. Different colored lines represent types of evidence for association: green, neighborhood evidence; red, fusion evidence; purple, experimental evidence; light blue, database evidence; black, coexpression evidence; blue, co-occurrence evidence; and yellow, text-mining evidence.
Figure 9
Figure 9
Conservation analysis of the ubiquitinated proteins in wheat. (A) All the identified ubiquitinated proteins in wheat compared with Oryza sativa, Arabidopsis thaliana. (B) Functional classification of the common ubiquitinated proteins identified in wheat, Oryza sativa, and Arabidopsis thaliana.

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