title: Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization.
abstract: cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequence (5'CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5'CS, and the presence of DCS-PK facilitates the formation of 5'-3' RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.
authors.affiliation: Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Zhong-Yu
authors.initials: ZY
authors.lastname: Liu
authors.forename: Xiao-Feng
authors.initials: XF
authors.lastname: Li
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
authors.forename: Yong-Qiang
authors.initials: YQ
authors.lastname: Deng
authors.forename: Hui
authors.initials: H
authors.lastname: Zhao
authors.forename: Hong-Jiang
authors.initials: HJ
authors.lastname: Wang
authors.forename: Qing
authors.initials: Q
authors.lastname: Ye
authors.forename: Shun-Ya
authors.initials: SY
authors.lastname: Zhu
authors.forename: Yang
authors.initials: Y
authors.lastname: Qiu
authors.forename: Xi
authors.initials: X
authors.lastname: Zhou
authors.forename: E-De
authors.initials: ED
authors.lastname: Qin
authors.forename: Cheng-Feng
authors.initials: CF
authors.lastname: Qin
mesh_terms: D000818:Animals; D001483:Base Sequence; D002213:Capsid / Q000737:chemistry* / Q000378:metabolism; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D003716:Dengue Virus / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005416:Flavivirus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D014779:Virus Replication
chemical_list: D036022:Capsid Proteins; D012367:RNA, Viral