scholarly journals Large-scale prediction of protein ubiquitination sites using a multimodal deep architecture

2018 ◽  
Vol 12 (S6) ◽  
Author(s):  
Fei He ◽  
Rui Wang ◽  
Jiagen Li ◽  
Lingling Bao ◽  
Dong Xu ◽  
...  
Author(s):  
Fynn M. Hansen ◽  
Maria C. Tanzer ◽  
Franziska Brüning ◽  
Isabell Bludau ◽  
Brenda A. Schulman ◽  
...  

SUMMARYProtein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. We developed a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identified 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells – double the number and quantitative accuracy of data dependent acquisition. Applied to TNF-alpha signaling, the workflow comprehensively captured known sites while adding many novel ones. A first systems-wide investigation of ubiquitination of the circadian cycle uncovered hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting novel connections between metabolism and circadian regulation.


2019 ◽  
Vol 15 (3) ◽  
pp. 1-26
Author(s):  
Ji Wang ◽  
Weidong Bao ◽  
Lei Zheng ◽  
Xiaomin Zhu ◽  
Philip S. Yu

2019 ◽  
Vol 14 (7) ◽  
pp. 614-620 ◽  
Author(s):  
Jiajing Chen ◽  
Jianan Zhao ◽  
Shiping Yang ◽  
Zhen Chen ◽  
Ziding Zhang

Background: As one of the most important reversible protein post-translation modification types, ubiquitination plays a significant role in the regulation of many biological processes, such as cell division, signal transduction, apoptosis and immune response. Protein ubiquitination usually occurs when ubiquitin molecule is attached to a lysine on a target protein, which is also known as “lysine ubiquitination”. Objective: In order to investigate the molecular mechanisms of ubiquitination-related biological processes, the crucial first step is the identification of ubiquitination sites. However, conventional experimental methods in detecting ubiquitination sites are often time-consuming and a large number of ubiquitination sites remain unidentified. In this study, a ubiquitination site prediction method for Arabidopsis thaliana was developed using a Support Vector Machine (SVM). Methods: We collected 3009 experimentally validated ubiquitination sites on 1607 proteins in A. thaliana to construct the training set. Three feature encoding schemes were used to characterize the sequence patterns around ubiquitination sites, including AAC, Binary and CKSAAP. The maximum Relevance and Minimum Redundancy (mRMR) feature selection method was employed to reduce the dimensionality of input features. Five-fold cross-validation and independent tests were used to evaluate the performance of the established models. Results: As a result, the combination of AAC and CKSAAP encoding schemes yielded the best performance with the accuracy and AUC of 81.35% and 0.868 in the independent test. We also generated an online predictor termed as AraUbiSite, which is freely accessible at: http://systbio.cau.edu.cn/araubisite. Conclusion: We developed a well-performed prediction tool for large-scale ubiquitination site identification in A. thaliana. It is hoped that the current work will speed up the process of identification of ubiquitination sites in A. thaliana and help to further elucidate the molecular mechanisms of ubiquitination in plants.


2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Yu-lin Huang ◽  
Peng-fei Zhang ◽  
Zhen Hou ◽  
Qiang Fu ◽  
Ming-xing Li ◽  
...  

Abstract Protein ubiquitination, a major and conserved post-translational modification, is known to play a critical regulatory role in many biological processes in eukaryotes. Although several ubiquitinated proteins have been found in buffalo (Bubalus bubalis) testis in our previous studies, large-scale profiling of buffalo testis ubiquitome has not been reported to date. In the present study, we first identified a global profiling of lysine ubiquitination of adult buffalo testis using a highly sensitive LC-MS/MS coupled with immune-affinity enrichment of ubiquitinated peptides. In total, 422 lysine ubiquitination sites were identified in 262 proteins in adult buffalo testis tissue. Bioinformatics analysis showed that the ubiquitinated proteins are involved in a variety of biological processes and diverse subcellular localizations. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein interaction network analysis indicated that proteasome, glycolysis/gluconeogenesis and gap junction pathways are modulated by protein ubiquitination in testis. Besides, 44 ubiquitinated proteins may involve in spermatogenesis according to the SpermatogenesisOnline database, of which, the ubiquitination of HSPA2 and UCHL1 were confirmed by Immunoprecipitation (IP)/Western blot analysis. Taken together, these data provide a global view of ubiquitome in buffalo testis for the first time, and serve as an important resource for exploring the physiological role especially spermatogenesis of lysine ubiquitination in testis in mammals.


Author(s):  
Xin Zhao ◽  
Guiguang Ding ◽  
Yuchen Guo ◽  
Jungong Han ◽  
Yue Gao

Cross-view retrieval, which focuses on searching images as response to text queries or vice versa, has received increasing attention recently. Cross-view hashing is to efficiently solve the cross-view retrieval problem with binary hash codes. Most existing works on cross-view hashing exploit multi-view embedding method to tackle this problem, which inevitably causes the information loss in both image and text domains. Inspired by the Generative Adversarial Nets (GANs), this paper presents a new model that is able to Turn Cross-view Hashing into single-view hashing (TUCH), thus enabling the information of image to be preserved as much as possible. TUCH is a novel deep architecture that integrates a language model network T for text feature extraction, a generator network G to generate fake images from text feature and a hashing network H for learning hashing functions to generate compact binary codes. Our architecture effectively unifies joint generative adversarial learning and cross-view hashing. Extensive empirical evidence shows that our TUCH approach achieves state-of-the-art results, especially on text to image retrieval, based on image-sentences datasets, i.e. standard IAPRTC-12 and large-scale Microsoft COCO.


2013 ◽  
Vol 7 ◽  
pp. JEN.S12453 ◽  
Author(s):  
Annelies Laeremans ◽  
Babs Van De Plas ◽  
Stefan Clerens ◽  
Gert Van Den Bergh ◽  
Lutgarde Arckens ◽  
...  

We explored differential protein expression profiles in the mouse forebrain at different stages of postnatal development, including 10-day (P10), 30-day (P30), and adult (Ad) mice, by large-scale screening of proteome maps using two-dimensional difference gel electrophoresis. Mass spectrometry analysis resulted in the identification of 251 differentially expressed proteins. Most molecular changes were observed between P10 compared to both P30 and Ad. Computational ingenuity pathway analysis (IPA) confirmed these proteins as crucial molecules in the biological function of nervous system development. Moreover, IPA revealed Semaphorin signaling in neurons and the protein ubiquitination pathway as essential canonical pathways in the mouse forebrain during postnatal development. For these main biological pathways, the transcriptional regulation of the age-dependent expression of selected proteins was validated by means of in situ hybridization. In conclusion, we suggest that proteolysis and neurite outgrowth guidance are key biological processes, particularly during early brain maturation.


2021 ◽  
Vol 118 (8) ◽  
pp. e2025421118
Author(s):  
Miao Li ◽  
Jiahuan Zheng ◽  
Gaopeng Li ◽  
Zexiong Lin ◽  
Dongliang Li ◽  
...  

Meiosis is a specialized cell division that creates haploid germ cells from diploid progenitors. Through differential RNA expression analyses, we previously identified a number of mouse genes that were dramatically elevated in spermatocytes, relative to their very low expression in spermatogonia and somatic organs. Here, we investigated in detail 1700102P08Rik, one of these genes, and independently conclude that it encodes a male germline-specific protein, in agreement with a recent report. We demonstrated that it is essential for pachynema progression in spermatocytes and named it male pachynema-specific (MAPS) protein. Mice lacking Maps (Maps−/−) suffered from pachytene arrest and spermatocyte death, leading to male infertility, whereas female fertility was not affected. Interestingly, pubertal Maps−/− spermatocytes were arrested at early pachytene stage, accompanied by defects in DNA double-strand break (DSB) repair, crossover formation, and XY body formation. In contrast, adult Maps−/− spermatocytes only exhibited partially defective crossover but nonetheless were delayed or failed in progression from early to mid- and late pachytene stage, resulting in cell death. Furthermore, we report a significant transcriptional dysregulation in autosomes and XY chromosomes in both pubertal and adult Maps−/− pachytene spermatocytes, including failed meiotic sex chromosome inactivation (MSCI). Further experiments revealed that MAPS overexpression in vitro dramatically decreased the ubiquitination levels of cellular proteins. Conversely, in Maps−/− pachytene cells, protein ubiquitination was dramatically increased, likely contributing to the large-scale disruption in gene expression in pachytene cells. Thus, MAPS is a protein essential for pachynema progression in male mice, possibly in mammals in general.


1999 ◽  
Vol 173 ◽  
pp. 243-248
Author(s):  
D. Kubáček ◽  
A. Galád ◽  
A. Pravda

AbstractUnusual short-period comet 29P/Schwassmann-Wachmann 1 inspired many observers to explain its unpredictable outbursts. In this paper large scale structures and features from the inner part of the coma in time periods around outbursts are studied. CCD images were taken at Whipple Observatory, Mt. Hopkins, in 1989 and at Astronomical Observatory, Modra, from 1995 to 1998. Photographic plates of the comet were taken at Harvard College Observatory, Oak Ridge, from 1974 to 1982. The latter were digitized at first to apply the same techniques of image processing for optimizing the visibility of features in the coma during outbursts. Outbursts and coma structures show various shapes.


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