title: Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.
abstract: OBJECTIVE
  To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS.
  
  
  METHODS
  Based on the studies about the genomic packaging signals of MHV and BCoV, especially the information about primary and secondary structures, the putative genomic packaging signal of SARS-CoV were analyzed by using bioinformatic tools. Multi-alignment for the genomic sequences was performed among SARS-CoV, MHV, BCoV, PEDV and HCoV 229E. Secondary structures of RNA sequences were also predicted for the identification of the possible genomic packaging signals. Meanwhile, the N and M proteins of all five viruses were analyzed to study the evolutionary relationship with genomic packaging signals.
  
  
  RESULTS
  The putative genomic packaging signal of SARS-CoV locates at the 3' end of ORF1b near that of MHV and BCoV, where is the most variable region of this gene. The RNA secondary structure of SARS-CoV genomic packaging signal is very similar to that of MHV and BCoV. The same result was also obtained in studying the genomic packaging signals of PEDV and HCoV 229E. Further more, the genomic sequence multi-alignment indicated that the locations of packaging signals of SARS-CoV, PEDV, and HCoV overlaped each other. It seems that the mutation rate of packaging signal sequences is much higher than the N protein, while only subtle variations for the M protein.
  
  
  CONCLUSIONS
  The probable genomic packaging signal of SARS-CoV is analogous to that of MHV and BCoV, with the corresponding secondary RNA structure locating at the similar region of ORF1b. The positions where genomic packaging signals exist have suffered rounds of mutations, which may influence the primary structures of the N and M proteins consequently.
authors.affiliation: Shanghai Center for Bioinformation Technology, Shanghai 201203, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Qin
authors.forename: Bin
authors.initials: B
authors.lastname: Xiong
authors.forename: Cheng
authors.initials: C
authors.lastname: Luo
authors.forename: Zong-Ming
authors.initials: ZM
authors.lastname: Guo
authors.forename: Pei
authors.initials: P
authors.lastname: Hao
authors.forename: Jiong
authors.initials: J
authors.lastname: Su
authors.forename: Peng
authors.initials: P
authors.lastname: Nan
authors.forename: Ying
authors.initials: Y
authors.lastname: Feng
authors.forename: Yi-Xiang
authors.initials: YX
authors.lastname: Shi
authors.forename: Xiao-Jing
authors.initials: XJ
authors.lastname: Yu
authors.forename: Xiao-Min
authors.initials: XM
authors.lastname: Luo
authors.forename: Kai-Xian
authors.initials: KX
authors.lastname: Chen
authors.forename: Xu
authors.initials: X
authors.lastname: Shen
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Shen
authors.forename: Jian-Ping
authors.initials: JP
authors.lastname: Zou
authors.forename: Guo-Ping
authors.initials: GP
authors.lastname: Zhao
authors.forename: Tie-Liu
authors.initials: TL
authors.lastname: Shi
authors.forename: Wei-Zhong
authors.initials: WZ
authors.lastname: He
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhong
authors.forename: Hua-Liang
authors.initials: HL
authors.lastname: Jiang
authors.forename: Yi-Xue
authors.initials: YX
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D028941:Coronavirus 229E, Human / Q000235:genetics; D017938:Coronavirus, Bovine / Q000235:genetics; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D006517:Murine hepatitis virus / Q000235:genetics; D019590:Nucleocapsid Proteins / Q000235:genetics*; D021382:Protein Sorting Signals / Q000235:genetics*; D017433:Protein Structure, Secondary; D034622:RNA Interference; D016372:RNA, Antisense / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics* / Q000302:isolation & purification; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D045169:Severe Acute Respiratory Syndrome / Q000821:virology*; D014763:Viral Matrix Proteins / Q000235:genetics*
chemical_list: D019590:Nucleocapsid Proteins; D021382:Protein Sorting Signals; D016372:RNA, Antisense; D012367:RNA, Viral; D014763:Viral Matrix Proteins