publication . Article . Other literature type . 2017

Comprehensive profiling of lysine ubiquitome reveals diverse functions of lysine ubiquitination in common wheat

Zhang, Ning; Zhang, Lingran; Shi, Chaonan; Tian, Qiuzhen; Lv, Guoguo; Wang, Ying; Cui, Dangqun; Chen, Feng;
Open Access English
  • Published: 01 Oct 2017 Journal: Scientific Reports (issn: 2045-2322, Copyright policy)
  • Publisher: Nature Publishing Group
Abstract
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 ...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Medicine, R, Science, Q, Article, Multidisciplinary, Homology (biology), Protein ubiquitination, Common wheat, Lysine, Oryza sativa, Ubiquitin, biology.protein, biology, Arabidopsis thaliana, biology.organism_classification, Interaction network, Biochemistry
Related Organizations
59 references, page 1 of 4

Kim, DY, Scalf, M, Smith, LM, Vierstra, RD. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Plant Cell. 2013; 25: 1523-40 [OpenAIRE] [PubMed] [DOI]

Kwon, SJ, Choi, EY, Choi, YJ, Ahn, JH, Park, OK. Proteomics studies of post-translational modifications in plants. J Exp Bot. 2006; 57: 1547-51 [OpenAIRE] [PubMed] [DOI]

Dikic, I, Wakatsuki, S, Walters, KJ. Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol. 2009; 10: 659-71 [OpenAIRE] [PubMed] [DOI]

Jiang, X, Chen, ZJ. The role of ubiquitylation in immune defence and pathogen evasion. Nat Rev Immunol. 2011; 12: 35-48 [OpenAIRE] [PubMed]

Kim, W. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell. 2011; 44: 325-40 [OpenAIRE] [PubMed] [DOI]

Sadanandom, A, Bailey, M, Ewan, R, Lee, J, Nelis, S. The ubiquitin-proteasome system: central modifier of plant signalling. New Phytol. 2012; 196: 13-28 [OpenAIRE] [PubMed] [DOI]

Xu, G, Paige, JS, Jaffrey, SR. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol. 2010; 28: 868-73 [OpenAIRE] [PubMed] [DOI]

Dreher, K, Callis, J. Ubiquitin, hormones and biotic stress in plants. Ann Bot. 2007; 99: 787-822 [OpenAIRE] [PubMed] [DOI]

Li, W. The U-Box/ARM E3 ligase PUB13 regulates cell death, defense, and flowering time in Arabidopsis. Plant Physiol. 2012; 159: 239-50 [OpenAIRE] [PubMed] [DOI]

Yates, G, Sadanandom, A. Ubiquitination in plant nutrient utilization. Front Plant Sci. 2013; 4: 452 [OpenAIRE] [PubMed] [DOI]

Peng, J. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003; 21: 921-6 [OpenAIRE] [PubMed] [DOI]

Danielsen, JM. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol Cell Proteomics. 2011; 10: M110 003590 [OpenAIRE] [PubMed] [DOI]

Meierhofer, D, Wang, X, Huang, L, Kaiser, P. Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res. 2008; 7: 4566-76 [OpenAIRE] [PubMed] [DOI]

Shi, Y. A data set of human endogenous protein ubiquitination sites. Mol Cell Proteomics. 2011; 10: M110 002089 [OpenAIRE] [PubMed] [DOI]

Wagner, SA. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics. 2011; 10: M111 013284 [OpenAIRE] [PubMed] [DOI]

59 references, page 1 of 4
Abstract
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 ...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Medicine, R, Science, Q, Article, Multidisciplinary, Homology (biology), Protein ubiquitination, Common wheat, Lysine, Oryza sativa, Ubiquitin, biology.protein, biology, Arabidopsis thaliana, biology.organism_classification, Interaction network, Biochemistry
Related Organizations
59 references, page 1 of 4

Kim, DY, Scalf, M, Smith, LM, Vierstra, RD. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Plant Cell. 2013; 25: 1523-40 [OpenAIRE] [PubMed] [DOI]

Kwon, SJ, Choi, EY, Choi, YJ, Ahn, JH, Park, OK. Proteomics studies of post-translational modifications in plants. J Exp Bot. 2006; 57: 1547-51 [OpenAIRE] [PubMed] [DOI]

Dikic, I, Wakatsuki, S, Walters, KJ. Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol. 2009; 10: 659-71 [OpenAIRE] [PubMed] [DOI]

Jiang, X, Chen, ZJ. The role of ubiquitylation in immune defence and pathogen evasion. Nat Rev Immunol. 2011; 12: 35-48 [OpenAIRE] [PubMed]

Kim, W. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell. 2011; 44: 325-40 [OpenAIRE] [PubMed] [DOI]

Sadanandom, A, Bailey, M, Ewan, R, Lee, J, Nelis, S. The ubiquitin-proteasome system: central modifier of plant signalling. New Phytol. 2012; 196: 13-28 [OpenAIRE] [PubMed] [DOI]

Xu, G, Paige, JS, Jaffrey, SR. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol. 2010; 28: 868-73 [OpenAIRE] [PubMed] [DOI]

Dreher, K, Callis, J. Ubiquitin, hormones and biotic stress in plants. Ann Bot. 2007; 99: 787-822 [OpenAIRE] [PubMed] [DOI]

Li, W. The U-Box/ARM E3 ligase PUB13 regulates cell death, defense, and flowering time in Arabidopsis. Plant Physiol. 2012; 159: 239-50 [OpenAIRE] [PubMed] [DOI]

Yates, G, Sadanandom, A. Ubiquitination in plant nutrient utilization. Front Plant Sci. 2013; 4: 452 [OpenAIRE] [PubMed] [DOI]

Peng, J. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003; 21: 921-6 [OpenAIRE] [PubMed] [DOI]

Danielsen, JM. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol Cell Proteomics. 2011; 10: M110 003590 [OpenAIRE] [PubMed] [DOI]

Meierhofer, D, Wang, X, Huang, L, Kaiser, P. Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res. 2008; 7: 4566-76 [OpenAIRE] [PubMed] [DOI]

Shi, Y. A data set of human endogenous protein ubiquitination sites. Mol Cell Proteomics. 2011; 10: M110 002089 [OpenAIRE] [PubMed] [DOI]

Wagner, SA. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics. 2011; 10: M111 013284 [OpenAIRE] [PubMed] [DOI]

59 references, page 1 of 4
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