Proteome-wide analysis of USP14 substrates revealed its role in hepatosteatosis via stabilization of

Zc3hav1l slc6a9 protein identified up regulated

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ZC3HAV1L SLC6A9 Protein identified Up-regulated protein Down-regulated protein 7647 50 108 Identified ubiquitin sites Quantified ubiquitin sites Up-regulated ubiquitin sites 392 6170 8679 GG Fig. 2 Quantitative proteomic pro fi ling for USP14 regulated proteins and interaction components. a The diagram shows the experimental process for the quantitative proteomics, ubiquitinome, protein protein interaction analysis of USP14. b Volcano plot of the protein abundance changes in response to USP14 KD. Average protein expression ratio of 4 replicates (log 2 transformed) between USP14 knockdown and wild-type HeLa cells was plotted against p -value by t -test ( - log 10 transformed). Cutoff of p = 0.05 and 1.2-fold change were marked by green and red lines, respectively. The fi gure below shows the total number of proteins identi fi ed as well as the number of up- and downregulated proteins. The detailed information on protein groups is listed in Supplementary Data 1. c Number of identi fi ed ubiquitin sites, quanti fi ed ubiquitin sites, and upregulated ubiquitin sites NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-07185-y ARTICLE NATURE COMMUNICATIONS | (2018)9:4770 | DOI: 10.1038/s41467-018-07185-y | 3
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was likely to be regulated by USP14. To check whether there was any particular amino acid preference adjacent to the ubiquitinated sites, we analyzed the anking sequences of upre- gulated ubiquitin sites using iceLogo software 27 . The result showed that glutamine and glutamic acid were notably over- represented close to the ubiquitin sites, whereas proline and leucine were less preferred near the ubiquitin sites (Supplemen- tary Fig. 2). Annotation of USP14 regulated proteome and ubiquitinome . To gain insight into the possible biological functions of USP14, we subjected the down- and up-regulated proteins in USP14 KD cells to bioinformatics enrichment analysis with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases by the ClueGO tool 28 . In addition to the enrichment of the known USP14 participated pathways, such as proteolysis, apoptosis and NF- κ B pathways (Fig. 3 a, Supplementary Data 3), our analysis revealed that USP14 could also plays a role in multiple previously less well-appreciated cellular functions, such as fatty acid and amino acid metabolisms, epidermal growth factor receptor (EGFR), peroxisome proliferator-activated recep- tor (PPAR), and p53 signaling pathways (Fig. 3 a, Supplementary Data 3). Notably, protein expression of the three key enzymes in the fatty acid synthesis pathway, ACLY, ACACA, FASN, and seven enzymes in the fatty acid degradation pathway were downregulated, which further indicated a possible role of USP14 in fatty acid metabolism (Fig. 3 c). Consistently, protein interac- tion network analysis of the USP14 regulated proteins using the STRING Database 29 also identi fi ed fatty acid metabolism as one of the highly interconnected clusters (Supplementary Fig. 3a and Supplementary Data 3).
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  • Winter '19
  • Robert S Kiss
  • Fatty acid metabolism, Fatty acid synthase, FASN

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