Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions.
Barcoded PLATO
Bromodomain inhibitor JQ1
Protein interaction
Ubiquitin-binding protein
Zika virus
Journal
Genomics, proteomics & bioinformatics
ISSN: 2210-3244
Titre abrégé: Genomics Proteomics Bioinformatics
Pays: China
ID NLM: 101197608
Informations de publication
Date de publication:
06 2019
06 2019
Historique:
received:
02
07
2018
revised:
24
10
2018
accepted:
21
12
2018
pubmed:
9
9
2019
medline:
21
12
2019
entrez:
9
9
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31494268
pii: S1672-0229(18)30126-8
doi: 10.1016/j.gpb.2018.12.010
pmc: PMC6818353
pii:
doi:
Substances chimiques
Antibodies
0
Peptides
0
Ubiquitin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
319-331Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM117838
Pays : United States
Organisme : NIAID NIH HHS
ID : R33 AI116180
Pays : United States
Informations de copyright
Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.
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