PMID- 25162025 OWN - NLM STAT- MEDLINE DCOM- 20150526 LR - 20211021 IS - 2314-6141 (Electronic) IS - 2314-6133 (Print) VI - 2014 DP - 2014 TI - The effects of the context-dependent codon usage bias on the structure of the nsp1alpha of porcine reproductive and respiratory syndrome virus. PG - 765320 LID - 10.1155/2014/765320 [doi] LID - 765320 AB - The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1alpha is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1 alpha 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 alpha on shaping the specific folding units (alpha-helix, beta-strand, and the coil) in the nsp1alpha were analyzed based on the structural information about this protease from protein data bank (PDB: 3IFU) and the nsp1 alpha of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1 alpha, we found that there is no link between the fluctuation of the overall tRNA abundance and the specific folding units in the nsp1alpha, and the low translation speed of ribosome caused by the tRNA abundance exists in the nsp1 alpha. The strong correlation between some synonymous codon usage and the specific folding units in the nsp1alpha was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1alpha. These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1alpha structure. FAU - Ding, Yao-zhong AU - Ding YZ AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - You, Ya-nan AU - You YN AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China. FAU - Sun, Dong-jie AU - Sun DJ AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China. FAU - Chen, Hao-tai AU - Chen HT AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Wang, Yong-lu AU - Wang YL AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Chang, Hui-yun AU - Chang HY AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Pan, Li AU - Pan L AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Fang, Yu-zhen AU - Fang YZ AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Zhang, Zhong-wang AU - Zhang ZW AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Zhou, Peng AU - Zhou P AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Lv, Jian-liang AU - Lv JL AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Liu, Xin-sheng AU - Liu XS AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Shao, Jun-jun AU - Shao JJ AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Zhao, Fu-rong AU - Zhao FR AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Lin, Tong AU - Lin T AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Stipkovits, Laszlo AU - Stipkovits L AD - RT-Europe Research Center Ltd., Budapest, Hungary. FAU - Pejsak, Zygmunt AU - Pejsak Z AD - Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantow, 24-100 Pulawy, Poland. FAU - Zhang, Yong-guang AU - Zhang YG AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. FAU - Zhang, Jie AU - Zhang J AD - State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China ; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140803 PL - United States TA - Biomed Res Int JT - BioMed research international JID - 101600173 RN - 0 (Codon) RN - 0 (Viral Nonstructural Proteins) RN - 9014-25-9 (RNA, Transfer) SB - IM MH - Amino Acid Sequence MH - Animals MH - Codon/*genetics MH - Porcine Reproductive and Respiratory Syndrome/*genetics/virology MH - Porcine respiratory and reproductive syndrome virus/chemistry/*genetics/pathogenicity MH - Protein Folding MH - RNA, Transfer/genetics MH - Swine MH - Viral Nonstructural Proteins/*chemistry/genetics PMC - PMC4137607 EDAT- 2014/08/28 06:00 MHDA- 2015/05/27 06:00 PMCR- 2014/08/03 CRDT- 2014/08/28 06:00 PHST- 2014/03/18 00:00 [received] PHST- 2014/06/05 00:00 [revised] PHST- 2014/06/19 00:00 [accepted] PHST- 2014/08/28 06:00 [entrez] PHST- 2014/08/28 06:00 [pubmed] PHST- 2015/05/27 06:00 [medline] PHST- 2014/08/03 00:00 [pmc-release] AID - 10.1155/2014/765320 [doi] PST - ppublish SO - Biomed Res Int. 2014;2014:765320. doi: 10.1155/2014/765320. Epub 2014 Aug 3.