In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease
Identifieur interne : 001016 ( Main/Exploration ); précédent : 001015; suivant : 001017In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease
Auteurs : Patrick C. Y. Woo [Hong Kong] ; Yi Huang [Hong Kong] ; Susanna K. P. Lau [Hong Kong] ; Hoi-Wah Tsoi [Hong Kong] ; Kwok-Yung Yuen [Hong Kong]Source :
- Microbiology and Immunology [ 0385-5600 ] ; 2005-10.
English descriptors
- Teeft :
- 3clpro, Accession, Acidic domain, Adrp, Amino, Amino acid residues, Amino acid sequences, Amino acids, Chan, Cleavage, Cleavage site, Cleavage sites, Complete genome sequence, Coronavirus, Coronavirus hku1, Coronavirus hku1 protease cleavage site, Coronavirus nucleocapsid protein, Coronaviruses, Cpdase, Cysteine, Cysteine residues, Genbank, Genbank accession, Genome, Genome sequence, Glycine, Guan, Helicase, Helicases, Histidine, Hku1, Hong kong, Human coronavirus, Infectious bronchitis virus, Infectious diseases, Multiple alignment, Murine, Mutagenesis studies, Novel cleavage site, Novel coronavirus, Nsp1, Nucleic, Nucleic acids, Other coronaviruses, Other group, Peiris, Pl1pro, Plpro, Polymerase, Polypeptide, Polyprotein, Poon, Protease, Putative, Putative cleavage sites, Putative helicase, Putative polypeptides, Rabbit hemorrhagic disease virus, Replicase, Replicase polyprotein, Respiratory syndrome, Sars, Sars coronavirus, Silico analysis, Slippery sequence, Tandem copies, Tsoi, Virol, Wong, Yuen, Ziebuhr.
Abstract
Recently we have described the discovery and complete genome sequence of a novel coronavirus associated with pneumonia, coronavirus HKU1 (CoV‐HKU1). In this study, a detailed in silico analysis of the ORF1ab, encoding the 7,182‐amino acid replicase polyprotein in the CoV‐HKU1 genome showed that the replicase polyprotein of CoV‐HKU1 is cleaved by its papain‐like proteases and 3C‐like protease (3CLpro) into 16 polypeptides homologous to the corresponding polypeptides in other coronaviruses. Surprisingly, analysis of the putative cleavage sites of the 3CLpro revealed a unique putative cleavage site. In all known coronaviruses, the P1 positions at the cleavage sites of the 3CLpro are occupied by glutamine. This is also observed in CoV‐HKU1, except for one site at the junction between nsp10 (helicase) and nsp11 (member of exonuclease family), where the P1 position is occupied by histidine. This amino acid substitution is due to a single nucleotide mutation in the CoV‐HKU1 genome, CAG/A to CAT. This probably represents a novel cleavage site because the same mutation was consistently observed in CoV‐HKU1 sequences from multiple specimens of different patients; the P2 and P1′‐P12′ positions of this cleavage site are consistent between CoV‐HKU1 and other coronaviruses; and as the helicase is one of the most conserved proteins in coronaviruses, cleavage between nsp10 and nsp11 should be an essential step for the generation of the mature functional helicase. Experiments, including purification and C‐terminal amino acid sequencing of the CoV‐HKU1 helicase and trans‐cleavage assays of the CoV‐HKU1 3CLpro will confirm the presence of this novel cleavage site.
Url:
DOI: 10.1111/j.1348-0421.2005.tb03681.x
Affiliations:
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scheme="Teeft" xml:lang="en"><term>3clpro</term><term>Accession</term><term>Acidic domain</term><term>Adrp</term><term>Amino</term><term>Amino acid residues</term><term>Amino acid sequences</term><term>Amino acids</term><term>Chan</term><term>Cleavage</term><term>Cleavage site</term><term>Cleavage sites</term><term>Complete genome sequence</term><term>Coronavirus</term><term>Coronavirus hku1</term><term>Coronavirus hku1 protease cleavage site</term><term>Coronavirus nucleocapsid protein</term><term>Coronaviruses</term><term>Cpdase</term><term>Cysteine</term><term>Cysteine residues</term><term>Genbank</term><term>Genbank accession</term><term>Genome</term><term>Genome sequence</term><term>Glycine</term><term>Guan</term><term>Helicase</term><term>Helicases</term><term>Histidine</term><term>Hku1</term><term>Hong kong</term><term>Human coronavirus</term><term>Infectious bronchitis virus</term><term>Infectious diseases</term><term>Multiple alignment</term><term>Murine</term><term>Mutagenesis studies</term><term>Novel cleavage site</term><term>Novel coronavirus</term><term>Nsp1</term><term>Nucleic</term><term>Nucleic acids</term><term>Other coronaviruses</term><term>Other group</term><term>Peiris</term><term>Pl1pro</term><term>Plpro</term><term>Polymerase</term><term>Polypeptide</term><term>Polyprotein</term><term>Poon</term><term>Protease</term><term>Putative</term><term>Putative cleavage sites</term><term>Putative helicase</term><term>Putative polypeptides</term><term>Rabbit hemorrhagic disease virus</term><term>Replicase</term><term>Replicase polyprotein</term><term>Respiratory syndrome</term><term>Sars</term><term>Sars coronavirus</term><term>Silico analysis</term><term>Slippery sequence</term><term>Tandem copies</term><term>Tsoi</term><term>Virol</term><term>Wong</term><term>Yuen</term><term>Ziebuhr</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">Recently we have described the discovery and complete genome sequence of a novel coronavirus associated with pneumonia, coronavirus HKU1 (CoV‐HKU1). In this study, a detailed in silico analysis of the ORF1ab, encoding the 7,182‐amino acid replicase polyprotein in the CoV‐HKU1 genome showed that the replicase polyprotein of CoV‐HKU1 is cleaved by its papain‐like proteases and 3C‐like protease (3CLpro) into 16 polypeptides homologous to the corresponding polypeptides in other coronaviruses. Surprisingly, analysis of the putative cleavage sites of the 3CLpro revealed a unique putative cleavage site. In all known coronaviruses, the P1 positions at the cleavage sites of the 3CLpro are occupied by glutamine. This is also observed in CoV‐HKU1, except for one site at the junction between nsp10 (helicase) and nsp11 (member of exonuclease family), where the P1 position is occupied by histidine. This amino acid substitution is due to a single nucleotide mutation in the CoV‐HKU1 genome, CAG/A to CAT. This probably represents a novel cleavage site because the same mutation was consistently observed in CoV‐HKU1 sequences from multiple specimens of different patients; the P2 and P1′‐P12′ positions of this cleavage site are consistent between CoV‐HKU1 and other coronaviruses; and as the helicase is one of the most conserved proteins in coronaviruses, cleavage between nsp10 and nsp11 should be an essential step for the generation of the mature functional helicase. Experiments, including purification and C‐terminal amino acid sequencing of the CoV‐HKU1 helicase and trans‐cleavage assays of the CoV‐HKU1 3CLpro will confirm the presence of this novel cleavage site.</div></front></TEI><affiliations><list><country><li>Hong Kong</li></country></list><tree><country name="Hong Kong"><noRegion><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name></noRegion><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><name sortKey="Tsoi, Hoi Ah" sort="Tsoi, Hoi Ah" uniqKey="Tsoi H" first="Hoi-Wah" last="Tsoi">Hoi-Wah Tsoi</name><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><name sortKey="Yuen, Kwok Ung" sort="Yuen, Kwok Ung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><name sortKey="Yuen, Kwok Ung" sort="Yuen, Kwok Ung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><name sortKey="Yuen, Kwok Ung" sort="Yuen, Kwok Ung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><name sortKey="Yuen, Kwok Ung" sort="Yuen, Kwok Ung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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