Systematic study of protein sumoylation: Development of a site‐specific predictor of SUMOsp 2.0

@article{Ren2009SystematicSO,
  title={Systematic study of protein sumoylation: Development of a site‐specific predictor of SUMOsp 2.0},
  author={Jian Ren and Xinjiao Gao and Changjiang Jin and Mei Zhu and Xiwei Wang and Andrew Shaw and Longping Wen and Xuebiao Yao and Yu Xue},
  journal={PROTEOMICS},
  year={2009},
  volume={9}
}
Protein sumoylation is an important reversible post‐translational modification on proteins, and orchestrates a variety of cellular processes. Recently, computational prediction of sumoylation sites has attracted much attention for its cost‐efficiency and power in genomic data mining. In this work, we developed SUMOsp 2.0, an accurate computing program with an improved group‐based phosphorylation scoring algorithm. Our analysis demonstrated that SUMOsp 2.0 has greater prediction accuracy than… 
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    2010 5th International Symposium on Health Informatics and Bioinformatics
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References

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SUMOsp: a web server for sumoylation site prediction
TLDR
A computational system SUMOsp—SUMOylation Sites Prediction, based on a manually curated dataset, integrating the results of two methods, GPS and MotifX, which were originally designed for phosphorylation site prediction that offers at least as good prediction performance as the only available method, SUMOplot, on a very large test set.
Defining the SUMO-modified Proteome by Multiple Approaches in Saccharomyces cerevisiae*
TLDR
A combination of yeast two-hybrid screening, a high copy suppressor selection with a SUMO isopeptidase mutant, and tandem mass spectrometry is used to define a large set of proteins that can be modified by SUMO in budding yeast, pointing to a surprisingly broad array of cellular processes regulated by SUMo conjugation.
Systematic Identification and Analysis of Mammalian Small Ubiquitin-like Modifier Substrates*
TLDR
The spectrum of human SUMO1 substrates identified in this screen suggests general roles of sumoylation in transcription, chromosome structure, and RNA processing, andSumoylation appears to regulate the functions of its substrates through multiple, context-dependent mechanisms.
Identification of Sumoylated Proteins by Systematic Immunoprecipitation of the Budding Yeast Proteome*
TLDR
This is the first attempt to immunoprecipitate a large fraction of the proteome of a eukaryote, and it demonstrates the utility of this method to identify post-translational modifications in the yeast proteome.
A Universal Strategy for Proteomic Studies of SUMO and Other Ubiquitin-like Modifiers*S
TLDR
The development of a universal strategy for proteomic studies of ubiquitin-like modifiers is reported, which determined that SUMO-1 andsumO-3 are stable proteins exhibiting half-lives of over 20 h, and supported that the SUMO paralogues are likely to be functionally distinct.
Global Analysis of Protein Sumoylation in Saccharomyces cerevisiae*
TLDR
Using a mass spectrometry-based approach, 271 new SUMO targets are identified that play roles in a diverse set of biological processes and greatly expand the scope of SUMO regulation in eukaryotic cells.
A Proteomic Study of SUMO-2 Target Proteins*
TLDR
SART1 and heterogeneous nuclear RNP M were shown to be genuine SUMO targets, confirming the validity of the approach and eight novel potential SUMO-2 target proteins were identified by at least two peptides.
A Proteomic Strategy for Gaining Insights into Protein Sumoylation in Yeast*S
TLDR
A proteomics approach was undertaken to identify the targets of sumoylation en mass using a double-affinity purification procedure from a Saccharomyces cerevisiae strain engineered to express tagged SUMO, resulting in 159 candidate sumoylated proteins being identified by two or more peptides.
A Proteome-wide Approach Identifies Sumoylated Substrate Proteins in Yeast*
TLDR
It is shown that several subunits of RNA polymerases I, II, and III, members of the transcription repression and chromatin remodeling machineries previously not known to be sumoylated, are modified by SUMO-1.
Global shifts in protein sumoylation in response to electrophile and oxidative stress.
TLDR
The results suggest that reactive electrophiles not only directly modify proteins but also lead to indirect changes in endogenous protein modifications that regulate protein functions.
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