title: Variation analysis of the severe acute respiratory syndrome coronavirus putative non-structural protein 2 gene and construction of three-dimensional model.
abstract: BACKGROUND
  The rapid transmission and high mortality rate made severe acute respiratory syndrome (SARS) a global threat for which no efficacious therapy is available now. Without sufficient knowledge about the SARS coronavirus (SARS-CoV), it is impossible to define the candidate for the anti-SARS targets. The putative non-structural protein 2 (nsp2) (3CL(pro), following the nomenclature by Gao et al, also known as nsp5 in Snidjer et al) of SARS-CoV plays an important role in viral transcription and replication, and is an attractive target for anti-SARS drug development, so we carried on this study to have an insight into putative polymerase nsp2 of SARS-CoV Guangdong (GD) strain.
  
  
  METHODS
  The SARS-CoV strain was isolated from a SARS patient in Guangdong, China, and cultured in Vero E6 cells. The nsp2 gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and cloned into eukaryotic expression vector pCI-neo (pCI-neo/nsp2). Then the recombinant eukaryotic expression vector pCI-neo/nsp2 was transfected into COS-7 cells using lipofectin reagent to express the nsp2 protein. The expressive protein of SARS-CoV nsp2 was analyzed by 7% sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). The nucleotide sequence and protein sequence of GD nsp2 were compared with that of other SARS-CoV strains by nucleotide-nucleotide basic local alignment search tool (BLASTN) and protein-protein basic local alignment search tool (BLASTP) to investigate its variance trend during the transmission. The secondary structure of GD strain and that of other strains were predicted by Garnier-Osguthorpe-Robson (GOR) Secondary Structure Prediction. Three-dimensional-PSSM Protein Fold Recognition (Threading) Server was employed to construct the three-dimensional model of the nsp2 protein.
  
  
  RESULTS
  The putative polymerase nsp2 gene of GD strain was amplified by RT-PCR. The eukaryotic expression vector (pCI-neo/nsp2) was constructed and expressed the protein in COS-7 cells successfully. The result of sequencing and sequence comparison with other SARS-CoV strains showed that nsp2 gene was relatively conservative during the transmission and total five base sites mutated in about 100 strains investigated, three of which in the early and middle phases caused synonymous mutation, and another two base sites variation in the late phase resulted in the amino acid substitutions and secondary structure changes. The three-dimensional structure of the nsp2 protein was successfully constructed.
  
  
  CONCLUSIONS
  The results suggest that polymerase nsp2 is relatively stable during the phase of epidemic. The amino acid and secondary structure change may be important for viral infection. The fact that majority of single nucleotide variations (SNVs) are predicted to cause synonymous, as well as the result of low mutation rate of nsp2 gene in the epidemic variations, indicates that the nsp2 is conservative and could be a target for anti-SARS drugs. The three-dimensional structure result indicates that the nsp2 protein of GD strain is high homologous with 3CL(pro) of SARS-CoV urbani strain, 3CL(pro) of transmissible gastroenteritis virus and 3CL(pro) of human coronavirus 229E strain, which further suggests that nsp2 protein of GD strain possesses the activity of 3CL(pro).
authors.affiliation: School of Public Health, Sun Yat-sen University, Guangzhou 510080, China. jiahailu@yahoo.com.cn
authors.forename: Jia-hai
authors.initials: JH
authors.lastname: Lu
authors.forename: Ding-mei
authors.initials: DM
authors.lastname: Zhang
authors.forename: Guo-ling
authors.initials: GL
authors.lastname: Wang
authors.forename: Zhong-min
authors.initials: ZM
authors.lastname: Guo
authors.forename: Chuan-hai
authors.initials: CH
authors.lastname: Zhang
authors.forename: Bing-yan
authors.initials: BY
authors.lastname: Tan
authors.forename: Li-ping
authors.initials: LP
authors.lastname: Ouyang
authors.forename: Li
authors.initials: L
authors.lastname: Lin
authors.forename: Yi-min
authors.initials: YM
authors.lastname: Liu
authors.forename: Wei-qing
authors.initials: WQ
authors.lastname: Chen
authors.forename: Wen-hua
authors.initials: WH
authors.lastname: Ling
authors.forename: Xin-bing
authors.initials: XB
authors.lastname: Yu
authors.forename: Nan-shan
authors.initials: NS
authors.lastname: Zhong
mesh_terms: D000818:Animals; D019556:COS Cells; D003546:Cysteine Endopeptidases / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D008958:Models, Molecular; D011994:Recombinant Proteins / Q000096:biosynthesis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry / Q000235:genetics*; D045169:Severe Acute Respiratory Syndrome / Q000188:drug therapy; D014961:X-Ray Diffraction
chemical_list: D011994:Recombinant Proteins; D003546:Cysteine Endopeptidases; C078306:nsP2 proteinase