Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions.
10.1016/j.gpb.2018.12.010
- Author:
Weili KONG
1
;
Tsuyoshi HAYASHI
1
;
Guillaume FICHES
1
;
Qikai XU
2
;
Mamie Z LI
2
;
Jianwen QUE
3
;
Shuai LIU
4
;
Wei ZHANG
4
;
Jun QI
5
;
Netty SANTOSO
1
;
Stephen J ELLEDGE
2
;
Jian ZHU
6
Author Information
1. Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.
2. Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
3. Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA.
4. Department of Chemistry, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA.
5. Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
6. Department of Pathology, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA. Electronic address: Jian.Zhu@osumc.edu.
- Publication Type:Journal Article
- Keywords:
Barcoded PLATO;
Bromodomain inhibitor JQ1;
Protein interaction;
Ubiquitin-binding protein;
Zika virus
- From:
Genomics, Proteomics & Bioinformatics
2019;17(3):319-331
- CountryChina
- Language:English
-
Abstract:
Proteins usually associate with other molecules physically to execute their functions. Identifying these interactions is important for the functional analysis of proteins. Previously, we reported the parallel analysis of translated ORFs (PLATO) to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the "bait" molecules, followed by the deep sequencing analysis of mRNA. However, the sample processing, from extraction of precipitated mRNA to generation of DNA libraries, includes numerous steps, which is tedious and may cause the loss of materials. Barcoded PLATO (PLATO-BC), an improved platform was further developed to test its application for protein interaction discovery. In this report, we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis (IBM). Tripartite motif containing 21 (TRIM21) was identified as a potentially new IBM autoantigen. We also expanded the application of PLATO-BC to identify protein interactions for JQ1, single ubiquitin peptide, and NS5 protein of Zika virus. From PLATO-BC analyses, we identified new protein interactions for these "bait" molecules. We demonstrate that Ewing sarcoma breakpoint region 1 (EWSR1) binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4. RIO kinase 3 (RIOK3), a newly identified ubiquitin-binding protein, is preferentially associated with K63-ubiquitin chain. We also find that Zika NS5 protein interacts with two previously unreported host proteins, par-3 family cell polarity regulator (PARD3) and chromosome 19 open reading frame 53 (C19orf53), whose attenuated expression benefits the replication of Zika virus. These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of "bait" molecules.
