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Xu J, Hu J, Wang J, Han Y, Hu Y, Wen J, Li Y, Ji J, Ye J, Zhang Z, Wei W, Li S, Wang J, Wang J, Yu J, Yang H. Genome organization of the SARS-CoV. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:226-35. [PMID: 15629035 PMCID: PMC5172239 DOI: 10.1016/s1672-0229(03)01028-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves. Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted. Seven PUPs had not been reported previously, and two of them were predicted to contain transmembrane regions. Eight ORFs partially overlapped with or embedded into those of known genes, revealing that the SARS-CoV genome is a small and compact one with overlapped coding regions. The most striking discovery is that an ORF locates on the minus strand. We have also annotated non-coding regions and identified the transcription regulating sequences (TRS) in the intergenic regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs.
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Affiliation(s)
- Jing Xu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jianfei Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Yujun Han
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yongwu Hu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- Wenzhou Medical College, Wenzhou 325003, China
| | - Jie Wen
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Yan Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ji
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jia Ye
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Zizhang Zhang
- College of Materials Science and Chemical Engineering, Yuquan Campus, Zhejiang University, Hangzhou 310027, China
| | - Wei Wei
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Songgang Li
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Jian Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Jun Yu
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
| | - Huanming Yang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
- James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China
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Denison MR, Zoltick PW, Leibowitz JL, Pachuk CJ, Weiss SR. Identification of polypeptides encoded in open reading frame 1b of the putative polymerase gene of the murine coronavirus mouse hepatitis virus A59. J Virol 1991; 65:3076-82. [PMID: 2033667 PMCID: PMC240963 DOI: 10.1128/jvi.65.6.3076-3082.1991] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The polypeptides encoded in open reading frame (ORF) 1b of the mouse hepatitis virus A59 putative polymerase gene of RNA 1 were identified in the products of in vitro translation of genome RNA. Two antisera directed against fusion proteins containing sequences encoded in portions of the 3'-terminal 2.0 kb of ORF 1b were used to immunoprecipitate p90, p74, p53, p44, and p32 polypeptides. These polypeptides were clearly different in electrophoretic mobility, antiserum reactivity, and partial protease digestion pattern from viral structural proteins and from polypeptides encoded in the 5' end of ORF 1a, previously identified by in vitro translation. The largest of these polypeptides had partial protease digestion patterns similar to those of polypeptides generated by in vitro translation of a synthetic mRNA derived from the 3' end of ORF 1b. The polypeptides encoded in ORF 1b accumulated more slowly during in vitro translation than polypeptides encoded in ORF 1a. This is consistent with the hypothesis that translation of gene A initiates at the 5' end of ORF 1a and that translation of ORF 1b occurs following a frameshift at the ORF 1a-ORF 1b junction. The use of in vitro translation of genome RNA and immunoprecipitation with antisera directed against various regions of the polypeptides encoded in gene A should make it possible to study synthesis and processing of the putative coronavirus polymerase.
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Affiliation(s)
- M R Denison
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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Pachuk CJ, Bredenbeek PJ, Zoltick PW, Spaan WJ, Weiss SR. Molecular cloning of the gene encoding the putative polymerase of mouse hepatitis coronavirus, strain A59. Virology 1989; 171:141-8. [PMID: 2545027 PMCID: PMC7130916 DOI: 10.1016/0042-6822(89)90520-5] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/1988] [Accepted: 03/08/1989] [Indexed: 01/01/2023]
Abstract
Complementary DNA (cDNA) libraries were constructed representing the genome RNA of the coronavirus mouse hepatitis virus, strain A59 (MHV-A59). From these libraries clones were selected to form a linear map across the entire gene A, the putative viral polymerase gene. This gene is approximately 23 kb in length, considerably larger than earlier estimates. Sequence analysis of the 5' terminal region of the genome indicates the presence of the 66-nucleotide leader that is found on all mRNAs. Secondary structure analysis of the 5' terminal region suggests that transcription of leader terminates in the region of nucleotide 66. The sequence of the first 2000 nucleotides is very similar to that reported for the closely related JHM strain of MHV and potentially encodes p28, a basic protein thought to be a component of the viral polymerase (L. Soe, C. K. Shieh, S. Baker, M. F. Chang, and M. M. C. Lai, 1987, J. Virol., 61, 3968-3976). Gene A contains two of the consensus sequences found in intergenic regions. One is adjacent to the 5' leader sequence and the other is upstream from the initiation codon for translation of gene B.
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Affiliation(s)
- C J Pachuk
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia 19104-6076
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