Comprehensive Proteomic Analysis of Lysine Ubiquitination in Seedling Leaves of <i>Nicotiana tabacum</i>

Zhan, Huaixu; Song, Liyun; Ali, Kamran; Han, Fang; Li, Bin; Zhou, Zhi; Liu, Tianbo; Song, Lili; Liu, Ying; Wang, Fenglong; Yang, Jinguang

doi:10.1021/acsomega.0c01741

Cited by 7 publications

(7 citation statements)

References 63 publications

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“…Additionally, we tested our architecture performance, as we prepared the data from Zhan, H. et al [ 79 ], and trained the same architecture. After the same steps, we obtained 1756 ubiquitination and 1756 non-ubiquitination Tobacco species sites which were chosen randomly.…”

Section: Resultsmentioning

confidence: 99%

UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites

Siraj

Lim

Tayara

et al. 2021

Genes

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Protein ubiquitylation is an essential post-translational modification process that performs a critical role in a wide range of biological functions, even a degenerative role in certain diseases, and is consequently used as a promising target for the treatment of various diseases. Owing to the significant role of protein ubiquitylation, these sites can be identified by enzymatic approaches, mass spectrometry analysis, and combinations of multidimensional liquid chromatography and tandem mass spectrometry. However, these large-scale experimental screening techniques are time consuming, expensive, and laborious. To overcome the drawbacks of experimental methods, machine learning and deep learning-based predictors were considered for prediction in a timely and cost-effective manner. In the literature, several computational predictors have been published across species; however, predictors are species-specific because of the unclear patterns in different species. In this study, we proposed a novel approach for predicting plant ubiquitylation sites using a hybrid deep learning model by utilizing convolutional neural network and long short-term memory. The proposed method uses the actual protein sequence and physicochemical properties as inputs to the model and provides more robust predictions. The proposed predictor achieved the best result with accuracy values of 80% and 81% and F-scores of 79% and 82% on the 10-fold cross-validation and an independent dataset, respectively. Moreover, we also compared the testing of the independent dataset with popular ubiquitylation predictors; the results demonstrate that our model significantly outperforms the other methods in prediction classification results.

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Section: Resultsmentioning

confidence: 99%

UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites

Siraj

Lim

Tayara

et al. 2021

Genes

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“…Many studies on ubiquitination proteomes have been recently performed in different species, including mammals, microbes, and plants ( Silmon de Monerri et al, 2015 ; Guo et al, 2017 ; Jiang et al, 2018 ; Li et al, 2018 ; Meng et al, 2018 ; Wang et al, 2019 ; Cai et al, 2020 ; Zhan et al, 2020 ; Zhang P. F. et al, 2020 ). The number of ubiquitination sites in papaya is more than for most reported organisms, suggesting a high degree of ubiquitination in papaya.…”

Section: Discussionmentioning

confidence: 99%

Quantitative Ubiquitylomic Analysis of the Dynamic Changes and Extensive Modulation of Ubiquitylation in Papaya During the Fruit Ripening Process

Bian

Huo

et al. 2022

Front. Plant Sci.

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Lysine ubiquitination is a highly conserved post-translational modification with diverse biological functions. However, there is little available information on lysine ubiquitination of non-histone proteins in papaya (Carica papaya L.). In total, 3,090 ubiquitination sites on 1,249 proteins with diverse localizations and functions were identified. Five conserved ubiquitinated K motifs were identified. Enrichment analysis showed that many Hsps were differentially ubiquitinated proteins (DUPs), suggesting an essential role of ubiquitination in degradation of molecular chaperone. Furthermore, 12 sugar metabolism-related enzymes were identified as DUPs, including an involvement of ubiquitination in nutrimental changes during the papaya ripening process. The ubiquitination levels of five fruit ripening-related DUPs, including one ethylene-inducible protein, two 1-aminocyclopropane-1-carboxylic acid oxidases, one endochitinase, and one cell wall invertase, were significantly changed during the ripening process. Our study extends the understanding of diverse functions for lysine ubiquitination in regulation of the papaya fruit ripening process.

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“…Despite the importance of the cytoplasmic FBPases in sugar metabolism, little is known regarding how their protein levels are regulated in plants. The results from several large-scale studies to screen for ubiquitinated proteins in leaf tissues identified several enzymes involved in photosynthesis and carbohydrate metabolism, including the Arabidopsis cyFBP and related proteins in several other plant species [ 55 , 56 , 57 , 58 ], suggesting that they may be subjected to ubiquitination. However, the results from those large-scale studies on the possible ubiquitination of FBPases were not validated by further analysis and more importantly the functional significance is unknown.…”

Section: Discussionmentioning

confidence: 99%

Arabidopsis Ubiquitin-Conjugating Enzymes UBC4, UBC5, and UBC6 Have Major Functions in Sugar Metabolism and Leaf Senescence

Wang

Cao

Willick

et al. 2022

IJMS

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The ubiquitin-conjugating enzyme (E2) is required for protein ubiquitination. Arabidopsis has 37 E2s grouped into 14 subfamilies and the functions for many of them are unknown. We utilized genetic and biochemical methods to study the roles of Arabidopsis UBC4, UBC5, and UBC6 of the E2 subfamily IV. The Arabidopsis ubc4/5/6 triple mutant plants had higher levels of glucose, sucrose, and starch than the control plants, as well as a higher protein level of a key gluconeogenic enzyme, cytosolic fructose 1,6-bisphosphatase 1 (cyFBP). In an in vitro assay, the proteasome inhibitor MG132 inhibited the degradation of recombinant cyFBP whereas ATP promoted cyFBP degradation. In the quadruple mutant ubc4/5/6 cyfbp, the sugar levels returned to normal, suggesting that the increased sugar levels in the ubc4/5/6 mutant were due to an increased cyFBPase level. In addition, the ubc4/5/6 mutant plants showed early leaf senescence at late stages of plant development as well as accelerated leaf senescence using detached leaves. Further, the leaf senescence phenotype remained in the quadruple ubc4/5/6 cyfbp mutant. Our results suggest that UBC4/5/6 have two lines of important functions, in sugar metabolism through regulating the cyFBP protein level and in leaf senescence likely through a cyFBP-independent mechanism.

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

Cited by 7 publications

References 63 publications

UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites

UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites

Quantitative Ubiquitylomic Analysis of the Dynamic Changes and Extensive Modulation of Ubiquitylation in Papaya During the Fruit Ripening Process

Arabidopsis Ubiquitin-Conjugating Enzymes UBC4, UBC5, and UBC6 Have Major Functions in Sugar Metabolism and Leaf Senescence

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