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KMID : 0381120180400090905
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Genes and Genomics
2018 Volume.40 No. 9 p.905 ~ p.912
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The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus
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Ma Xiao-Xia
Wang Yi-Ning
Cao Xiao-An
Li Xue-Rui
Liu Yong-Sheng
Zhou Jian-Hua
Cai Xue-Peng
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Abstract
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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 (α-helix, β-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 (β-strand → coil, coil → β-strand, α-helix → coil, coil → α-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (β-strand → coil and coil → β-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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KEYWORD
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Peste des petits ruminants virus, PPRV, Nucleocapsid, Synonymous codon usage, tRNA abundance, Secondary structure
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