The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus

文献类型： 外文期刊

第一作者： Ma, Xiao-xia

作者： Ma, Xiao-xia;Wang, Yi-ning;Cao, Xiao-an;Li, Xue-rui;Liu, Yong-sheng;Zhou, Jian-hua;Cai, Xue-peng;Ma, Xiao-xia;Ma, Xiao-xia

作者机构：

关键词： Peste des petits ruminants virus; PPRV; Nucleocapsid; Synonymous codon usage; tRNA abundance; Secondary structure

期刊名称：GENES & GENOMICS （ 影响因子：1.839； 五年影响因子：1.329 ）

ISSN： 1976-9571

年卷期： 2018 年 40 卷 9 期

页码：

收录情况： SCI

摘要： The nucleocapsid (N) protein of peste des petits ruminants virus (PPRV) with a conserved amino acid usage pattern plays an important role in viral replication. The primary objective of this study was to estimate roles of synonymous codon usages of PPRV N gene and tRNA abundances of host in the formation of secondary structure of N protein. The potential effects of synonymous codon usages of N gene and tRNA abundances of host on shaping different folding units (alpha-helix, beta-strand and the coil) in N protein were estimated, based on the information about the modeling secondary structure of PPRV N protein. The synonymous codon usage bias was found in different folding units in PPRV N protein. To better understand the role of translation speed caused by variant tRNA abundances in shaping the specific folding unit in N protein, we modeled the changing trends of tRNA abundance at the transition boundaries from one folding unit to another folding unit (beta-strand -> coil, coil -> beta-strand, alpha-helix -> coil, coil -> alpha-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (beta-strand -> coil and coil -> beta-strand) in PPRV N protein. Our findings suggested that viral synonymous codon usage bias and cellular tRNA abundance variation might have potential effects on the formation of secondary structure of PPRV N protein.

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