Dataset Information

The effects of the context-dependent codon usage bias on the structure of the nsp1? of porcine reproductive and respiratory syndrome virus.

ABSTRACT: The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1? is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1 ? gene in the formation of this protease. The effects of tRNA abundance of the pigs and the synonymous codon usage and the context-dependent codon bias (CDCB) of the nsp1 ? on shaping the specific folding units (?-helix, ?-strand, and the coil) in the nsp1? were analyzed based on the structural information about this protease from protein data bank (PDB: 3IFU) and the nsp1 ? of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1 ?, we found that there is no link between the fluctuation of the overall tRNA abundance and the specific folding units in the nsp1?, and the low translation speed of ribosome caused by the tRNA abundance exists in the nsp1 ?. The strong correlation between some synonymous codon usage and the specific folding units in the nsp1? was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1?. These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1? structure.

SUBMITTER: Ding YZ

PROVIDER: S-EPMC4137607 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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The effects of the context-dependent codon usage bias on the structure of the nsp1α of porcine reproductive and respiratory syndrome virus.

Ding Yao-zhong YZ You Ya-nan YN Sun Dong-jie DJ Chen Hao-tai HT Wang Yong-lu YL Chang Hui-yun HY Pan Li L Fang Yu-zhen YZ Zhang Zhong-wang ZW Zhou Peng P Lv Jian-liang JL Liu Xin-sheng XS Shao Jun-jun JJ Zhao Fu-rong FR Lin Tong T Stipkovits Laszlo L Pejsak Zygmunt Z Zhang Yong-guang YG Zhang Jie J

BioMed research international 20140803

The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1α is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1 α gene in the formation of this protease. The effects of tRNA abundance of the pigs and the synonymous codon usage and the context-dependent codon bias (CDCB) of the nsp1 α on shaping the specific folding units (α-helix, β-strand, and the coil) in the nsp1α were analyzed based on th ...[more]

PMID: 25162025

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Project description:Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in pigs of all ages and reproductive failure in sows, resulting in great economic losses to the swine industry. In this work, we identified the interaction between PSMB4 and PRRSV Nsp1α by yeast two-hybrid screening. The PSMB4-Nsp1α interaction was further confirmed by coimmunoprecipitation, glutathione S-transferase (GST) pulldown, and laser confocal experiments. The PCPα domain (amino acids 66 to 166) of Nsp1α and the C-terminal domain (amino acids 250 to 264) of PSMB4 were shown to be critical for the PSMB4-Nsp1α interaction. PSMB4 overexpression reduced PRRSV replication, whereas PSMB4 knockdown elicited opposing effects. Mechanistically, PSMB4 targeted K169 in Nsp1α for K63-linked ubiquitination and targeted Nsp1α for autolysosomal degradation by interacting with LC3 to enhance the activation of the lysosomal pathway. Meanwhile, we found that PSMB4 activated the NF-κB signaling pathway to produce type I interferons by downregulating the expression of IκBα and p-IκBα. In conclusion, our data revealed a new mechanism of PSMB4-mediated restriction of PRRSV replication, whereby PSMB4 was found to induce Nsp1α degradation and type I interferon expression, in order to impede the replication of PRRSV. IMPORTANCE In the swine industry, PRRSV is a continuous threat, and the current vaccines are not effective enough to block it. This study determined that PSMB4 plays an antiviral role against PRRSV. PSMB4 was found to interact with PRRSV Nsp1α, mediate K63-linked ubiquitination of Nsp1α at K169, and thus trigger its degradation via the lysosomal pathway. Additionally, PSMB4 activated the NF-κB signaling pathway to produce type I interferons by downregulating the expression of IκBα and p-IκBα. This study extends our understanding of the proteasome subunit PSMB4 against PRRSV replication and will contribute to the development of new antiviral strategies.

Dataset Information

The effects of the context-dependent codon usage bias on the structure of the nsp1? of porcine reproductive and respiratory syndrome virus.

Publications

The effects of the context-dependent codon usage bias on the structure of the nsp1α of porcine reproductive and respiratory syndrome virus.

Similar Datasets

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