Global Analysis of SUMO-binding proteins identifies SUMOylation as a key regulator of the INO80 chromatin remodeling complex

microarray;SUMOylation;INO80;Biochemistry

Cox, EricNathans, Jeremy ;

Johns Hopkins University

关键词: microarray;    SUMOylation;    INO80;    Biochemistry;   

Others  :  https://jscholarship.library.jhu.edu/bitstream/handle/1774.2/40195/COX-DISSERTATION-2014.pdf?sequence=1&isAllowed=y

瑞士|英语

来源: JOHNS HOPKINS DSpace Repository

【 摘 要 】

The functional protein microarray is a powerful and versatile systems biology and proteomics tool that allows the rapid activity profiling of thousands of proteins in parallel. Applications of functional protein microarrays range from the identification of protein- binding properties, to surveying targets of posttranslational modifications, to uncovering novel enzymatic activities. Since the development of the yeast proteome microarray over 10 years ago, more recent work has seen the development of complete and near-complete proteome arrays representing viruses, bacteria and plants. However, most existing human protein microarrays are comprised of only a minority of the human proteome. We have recently developed a human proteome microarray, the HuProt array, which includes nearly 20,000 full-length human proteins.SUMOylation is an essential posttranslational modification in most organisms that is thought to function through its ability to modulate the protein-protein interactions of a SUMO target protein. Accordingly, the function of SUMOylation can be better understood through the identification of SUMO-modified targets as well as downstream SUMO- interacting proteins. Recently, we have conducted SUMOylation assays using the HuProt microarray to identify numerous previously uncharacterized SUMO E3 ligase-dependent substrates using a subset of human SUMO E3 ligases. In order to identify novel SUMO- interacting proteins, we developed a SUMO-binding assay using the human proteome microarray. We then integrated SUMO-binding and SUMOylation data, as well as protein- protein interaction data from publicly available databases to perform network motif analysis. We focused on a single network motif we termed a SUMOmod PPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E and that TFPT is a SUMO substrate both in vitro and in vivo. We then went on to demonstrate a key role for SUMOylation in mediating the interaction between these two proteins, both in vitro and in vivo. By demonstrating a key role for SUMOylation in regulating the INO80 chromatin remodeling complex, this work illustrates the power of bioinformatics analysis of large datasets in predicting novel biological phenomena.