title: Application of an Integrated Omics Approach for Identifying Host Proteins That Interact With Odontoglossum ringspot virus Capsid Protein.
abstract: The glutamic acid at position 100 (E(100)) in the capsid protein (CP) of Odontoglossum ringspot virus (ORSV) plays an important role in long-distance viral movement in Nicotiana benthamiana. The ORSV(E100A) mutant, which has a glutamic acid to alanine substitution, shows a loss of systemic infectivity in N. benthamiana. Transmission electron microscopy and size-exclusion chromatography assays showed that E(100) is essential for CP-CP interaction and viral particle assembly. To identify the ORSV triggering or response genes and CP-interacting proteins (CP-IP), an integrated omics approach based on next-generation sequencing and proteomics profiling was used in this study. The whole-transcriptomes of healthy and ORSV-infected leaves of N. benthamiana were analyzed, and the gene information was used to create a N. benthamiana protein database that was used for protein identification following mass spectrometry analysis. The integrated omics approach identified several putative host proteins that interact with ORSV CP(WT) and were categorized as photosystem subunits, defense-associated proteins, and cell division components. The expression pattern and CP interaction of these CP-IP were examined by semiquantitative reverse transcription polymerase chain reaction and an in vitro binding assay, respectively, to verify the in silico data. Among these proteins, a proteinase inhibitor of N. benthamiana (NbPI2) was highly associated with CP(E100A) as compared with CP(WT), and NbPI1 and NbPI2 were highly induced in ORSV-infected plants. NbPI1- and NbPI2-silenced plants (via a Tobacco rattle virus-induced gene-silencing system) did not exhibit a difference in ORSV infection. Thus, whether NbPI1 and NbPI2 play a role in plant immunity requires further investigation. In summary, the integrated omics approach provides massive and valuable information to identify the ORSV CP-IP and these CP-IP will help us to understand the movement of this virus and plant-virus interaction.
authors.affiliation: 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;|2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan;
authors.forename: Pin-Chun
authors.initials: PC
authors.lastname: Lin
authors.affiliation: 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Hu
authors.affiliation: 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;
authors.forename: Shu-Chuan
authors.initials: SC
authors.lastname: Lee
authors.affiliation: 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan;|5 Institute of Plant Biology and Department of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;
authors.forename: Ying-Lan
authors.initials: YL
authors.lastname: Chen
authors.affiliation: 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan;
authors.forename: Chi-Ying
authors.initials: CY
authors.lastname: Lee
authors.affiliation: 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan;
authors.forename: Yet-Ran
authors.initials: YR
authors.lastname: Chen
authors.affiliation: 6 Department of Agronomy, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan.
authors.forename: Li-Yu Daisy
authors.initials: LY
authors.lastname: Liu
authors.affiliation: 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;
authors.forename: Po-Yen
authors.initials: PY
authors.lastname: Chen
authors.affiliation: 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan;|3 Genome and Systems Biology Degree Program, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;|4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan;
authors.forename: Shih-Shun
authors.initials: SS
authors.lastname: Lin
authors.affiliation: 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan;
authors.forename: Ya-Chun
authors.initials: YC
authors.lastname: Chang
mesh_terms: D000595:Amino Acid Sequence; D036022:Capsid Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D023281:Genomics; D018698:Glutamic Acid; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000821:virology*; D057865:Plant Immunity; D018515:Plant Leaves / Q000821:virology; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D025941:Protein Interaction Mapping; D011993:Recombinant Fusion Proteins; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014026:Nicotiana / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D017898:Tobamovirus / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D036022:Capsid Proteins; D010940:Plant Proteins; D011993:Recombinant Fusion Proteins; D018698:Glutamic Acid