CPLM: a database of protein lysine modifications
Zexian Liu1, Yongbo Wang, Tianshun Gao
1Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
Nucleic Acids Research
|November 12, 2013
Summary
The Compendium of Protein Lysine Modifications (CPLM) database now includes 12 types of protein lysine modifications (PLMs). This resource reveals extensive crosstalk between different PLMs on the same lysine residues, impacting biological processes.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Protein lysine modifications (PLMs) are crucial for regulating diverse biological processes.
- Existing databases primarily focused on specific PLMs, like acetylation.
Purpose of the Study:
- To create an integrated database (CPLM) for a comprehensive collection of experimentally identified PLMs.
- To analyze the co-occurrence and crosstalk patterns of various PLMs on lysine residues.
Main Methods:
- Manual curation of experimentally identified PLM substrates and sites.
- Integration of data from the Compendium of Protein Lysine Acetylation (CPLA) database.
- Systematic analysis of PLM co-occurrence patterns.
Main Results:
- The CPLM database encompasses 203,972 modification events across 12 PLM types in 45,748 proteins from 122 species.
- Identified 76 types of PLM co-occurrences, with acetylation and ubiquitination being the most frequent crosstalk.
- Significant overlap observed between acetylation and ubiquitination at specific lysine sites.
Conclusions:
- The CPLM database provides a valuable resource for studying the complex regulatory roles of PLMs.
- Extensive PLM crosstalk suggests dynamic and competitive regulation of lysine residues.
- Further research into PLM crosstalk is warranted to understand intricate biological mechanisms.
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