ICysMod: an integrative database for protein cysteine modifications in eukaryotes. Issue 5 (7th January 2021)

• Record Type: Journal Article
• Authors: Wang, Panqin; Zhang, Qingfeng; Li, Shihua; Cheng, Ben; Xue, Han; Wei, Zhen; Shao, Tian; Liu, Ze-Xian; Cheng, Han; Wang, Zhenlong
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 5(2021)
• Publication Date: 2021-01-07
• Subjects: post-translational modifications (PTMs) -- protein cysteine modifications (PCMs) -- PCM events -- sequence features -- crosstalk; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbaa400
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108 030 PCM events for 85 747 experimentally identified sites on 31 483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2 H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37 841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info .