title: Structure and function analysis of nucleocapsid protein of tomato spotted wilt virus interacting with RNA using homology modeling.
abstract: The nucleocapsid (N) protein of tomato spotted wilt virus (TSWV) plays key roles in assembling genomic RNA into ribonucleoprotein (RNP), which serves as a template for both viral gene transcription and genome replication. However, little is known about the molecular mechanism of how TSWV N interacts with genomic RNA. In this study, we demonstrated that TSWV N protein forms a range of higher ordered oligomers. Analysis of the RNA binding behavior of N protein revealed that no specific oligomer binds to RNA preferentially, instead each type of N oligomer is able to bind RNA. To better characterize the structure and function of N protein interacting with RNA, we constructed homology models of TSWV N and N-RNA complexes. Based on these homology models, we demonstrated that the positively charged and polar amino acids in its predicted surface cleft of TSWV N are critical for RNA binding. Moreover, by N-RNA homology modeling, we found that the RNA component is deeply embedded in the predicted protein cleft; consistently, TSWV N-RNA complexes are relatively resistant to digestion by RNase. Collectively, using homology modeling, we determined the RNA binding sites on N and found a new protective feature for N protein. Our findings also provide novel insights into the molecular details of the interaction of TSWV N with RNA components.
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and.
authors.forename: Zhike
authors.initials: Z
authors.lastname: Feng
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and.
authors.forename: Jianyan
authors.initials: J
authors.lastname: Wu
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and.
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and.
authors.forename: Gang
authors.initials: G
authors.lastname: Lu
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and.
authors.forename: Min
authors.initials: M
authors.lastname: Zhu
authors.affiliation: the Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China.
authors.forename: Bi
authors.initials: B
authors.lastname: Wang
authors.affiliation: the College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095 and.
authors.forename: Xiang
authors.initials: X
authors.lastname: Mao
authors.affiliation: From the Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and taoxiaorong@njau.edu.cn.
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Tao
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D015153:Blotting, Western; D047369:Chromatin Immunoprecipitation; D024202:Electrophoretic Mobility Shift Assay; D047468:Immunoprecipitation; D018551:Solanum lycopersicum / Q000235:genetics / Q000378:metabolism / Q000821:virology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019590:Nucleocapsid Proteins / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017865:Tospovirus / Q000502:physiology*
chemical_list: D019590:Nucleocapsid Proteins; D012333:RNA, Messenger; D012367:RNA, Viral; C099603:nucleocapsid protein, Tospovirus
keywords: Homology Modeling; Negative-strand RNA Virus; Nucleocapsid; Plant Virus; RNA; Ribonucleoprotein; Tomato Spotted Wilt Virus; Virus Assembly