In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease
Identifieur interne : 000616 ( Istex/Corpus ); précédent : 000615; suivant : 000617In 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 ; Yi Huang ; Susanna K. P. Lau ; Hoi-Wah Tsoi ; Kwok-Yung YuenSource :
- 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
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ISTEX:CB350233D709FE608543F1EF2F2AC5F0B0C14CDDLe document en format XML
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Y." last="Woo">Patrick C. Y. Woo</name><affiliation><mods:affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</mods:affiliation></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><mods:affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</mods:affiliation></affiliation></author><author><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><affiliation><mods:affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</mods:affiliation></affiliation></author><author><name sortKey="Tsoi, Hoi Ah" sort="Tsoi, Hoi Ah" uniqKey="Tsoi H" first="Hoi-Wah" last="Tsoi">Hoi-Wah Tsoi</name><affiliation><mods:affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</mods:affiliation></affiliation></author><author><name sortKey="Yuen, Kwok Ung" sort="Yuen, Kwok Ung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><mods:affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: hkumicro@hkucc.hku.hk</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Microbiology and Immunology</title><title level="j" type="alt">MICROBIOLOGY AND IMMUNOLOGY</title><idno type="ISSN">0385-5600</idno><idno type="eISSN">1348-0421</idno><imprint><biblScope unit="vol">49</biblScope><biblScope unit="issue">10</biblScope><biblScope unit="page" from="899">899</biblScope><biblScope unit="page" to="908">908</biblScope><biblScope unit="page-count">10</biblScope><date type="published" when="2005-10">2005-10</date></imprint><idno type="ISSN">0385-5600</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0385-5600</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords 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><istex><corpusName>wiley</corpusName><keywords><teeft><json:string>coronavirus</json:string><json:string>coronaviruses</json:string><json:string>putative</json:string><json:string>3clpro</json:string><json:string>genome</json:string><json:string>other coronaviruses</json:string><json:string>sars</json:string><json:string>helicase</json:string><json:string>polyprotein</json:string><json:string>replicase</json:string><json:string>hku1</json:string><json:string>virol</json:string><json:string>chan</json:string><json:string>polymerase</json:string><json:string>amino</json:string><json:string>yuen</json:string><json:string>replicase polyprotein</json:string><json:string>cleavage site</json:string><json:string>nsp1</json:string><json:string>adrp</json:string><json:string>protease</json:string><json:string>cysteine</json:string><json:string>helicases</json:string><json:string>glycine</json:string><json:string>wong</json:string><json:string>cleavage</json:string><json:string>amino acids</json:string><json:string>poon</json:string><json:string>polypeptide</json:string><json:string>respiratory syndrome</json:string><json:string>peiris</json:string><json:string>guan</json:string><json:string>genbank</json:string><json:string>accession</json:string><json:string>hong kong</json:string><json:string>nucleic acids</json:string><json:string>coronavirus hku1</json:string><json:string>ziebuhr</json:string><json:string>murine</json:string><json:string>tsoi</json:string><json:string>histidine</json:string><json:string>cpdase</json:string><json:string>amino acid residues</json:string><json:string>pl1pro</json:string><json:string>plpro</json:string><json:string>multiple alignment</json:string><json:string>human coronavirus</json:string><json:string>genbank accession</json:string><json:string>novel coronavirus</json:string><json:string>slippery sequence</json:string><json:string>silico analysis</json:string><json:string>cysteine residues</json:string><json:string>amino acid sequences</json:string><json:string>novel cleavage site</json:string><json:string>acidic domain</json:string><json:string>sars coronavirus</json:string><json:string>nucleic</json:string><json:string>rabbit hemorrhagic disease virus</json:string><json:string>coronavirus hku1 protease cleavage site</json:string><json:string>putative helicase</json:string><json:string>mutagenesis studies</json:string><json:string>tandem copies</json:string><json:string>other group</json:string><json:string>putative polypeptides</json:string><json:string>genome sequence</json:string><json:string>infectious bronchitis virus</json:string><json:string>cleavage sites</json:string><json:string>putative cleavage sites</json:string><json:string>complete genome sequence</json:string><json:string>infectious diseases</json:string><json:string>coronavirus nucleocapsid protein</json:string></teeft></keywords><author><json:item><name>Patrick C.Y. Woo</name><affiliations><json:string>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</json:string><json:string>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</json:string><json:string>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</json:string></affiliations></json:item><json:item><name>Yi Huang</name><affiliations><json:string>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</json:string></affiliations></json:item><json:item><name>Susanna K.P. Lau</name><affiliations><json:string>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</json:string><json:string>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</json:string><json:string>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</json:string></affiliations></json:item><json:item><name>Hoi‐wah Tsoi</name><affiliations><json:string>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</json:string></affiliations></json:item><json:item><name>Kwok‐yung Yuen</name><affiliations><json:string>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</json:string><json:string>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</json:string><json:string>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</json:string><json:string>E-mail: hkumicro@hkucc.hku.hk</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>coronavirus HKU1</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ORF1ab</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>3C‐like protease</value></json:item></subject><articleId><json:string>MIM03681</json:string></articleId><arkIstex>ark:/67375/WNG-0NF3QX7S-2</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><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.</abstract><qualityIndicators><score>9.988</score><pdfWordCount>5009</pdfWordCount><pdfCharCount>32365</pdfCharCount><pdfVersion>1.6</pdfVersion><pdfPageCount>10</pdfPageCount><pdfPageSize>595 x 788 pts</pdfPageSize><pdfWordsPerPage>501</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>true</refBibsNative><abstractWordCount>249</abstractWordCount><abstractCharCount>1673</abstractCharCount><keywordCount>3</keywordCount></qualityIndicators><title>In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease</title><pmid><json:string>16237267</json:string></pmid><genre><json:string>article</json:string></genre><host><title>Microbiology and Immunology</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1348-0421</json:string></doi><issn><json:string>0385-5600</json:string></issn><eissn><json:string>1348-0421</json:string></eissn><publisherId><json:string>MIM</json:string></publisherId><volume>49</volume><issue>10</issue><pages><first>899</first><last>908</last><total>10</total></pages><genre><json:string>journal</json:string></genre><subject><json:item><value>Article</value></json:item><json:item><value>Articles</value></json:item></subject></host><namedEntities><unitex><date><json:string>2002</json:string><json:string>2003</json:string><json:string>2013-10-31</json:string><json:string>2004</json:string></date><geogName></geogName><orgName><json:string>University of Hong Kong</json:string><json:string>Tsinghua University</json:string><json:string>Department of Microbiology, The University of Hong Kong, Room</json:string><json:string>Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food</json:string><json:string>And HKU/UCH SARS Study Group</json:string><json:string>Suen Chi Sun Charitable Foundation and Infectious Diseases and William</json:string><json:string>Queen Mary Hospital Compound, Pokfulam Road, Hong Kong</json:string><json:string>State Key Laboratory of Emerging Infectious Diseases</json:string><json:string>And SARS Study Group</json:string><json:string>Research Centre of Infection and Immunology</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Yi Huang</json:string><json:string>Hong Kong</json:string><json:string>Professor Zihe</json:string><json:string>Rao</json:string><json:string>AL Fig</json:string><json:string>Kwok</json:string><json:string>K.P. 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ref="https://scientific-publisher.data.istex.fr/ark:/67375/H02-QW5Q88H5-V">Wiley Publishing Ltd</publisher><availability><licence>© owned by Center for Academic Publications Japan (Publisher)</licence></availability><date type="published" when="2005-10"></date></publicationStmt><notesStmt><note type="content-type" subtype="article" source="article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</note><note type="publication-type" subtype="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="article"><analytic><title level="a" type="main">In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease</title><author xml:id="author-0000"><persName><forename type="first">Patrick C.Y.</forename><surname>Woo</surname></persName><affiliation><orgName type="division">Department of Microbiology, The University of Hong Kong</orgName><orgName type="institution">University Pathology Building</orgName><address><street>Queen Mary Hospital</street><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation><affiliation><orgName type="division">Research Centre of Infection and Immunology, Faculty of Medicine</orgName><orgName type="institution">The University of Hong Kong</orgName><address><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation><affiliation><orgName type="division">State Key Laboratory of Emerging Infectious Diseases</orgName><orgName type="institution">The University of Hong Kong</orgName><address><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">Yi</forename><surname>Huang</surname></persName><affiliation><orgName type="division">Department of Microbiology, The University of Hong Kong</orgName><orgName type="institution">University Pathology Building</orgName><address><street>Queen Mary Hospital</street><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Susanna K.P.</forename><surname>Lau</surname></persName><affiliation><orgName type="division">Department of Microbiology, The University of Hong Kong</orgName><orgName type="institution">University Pathology Building</orgName><address><street>Queen Mary Hospital</street><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation><affiliation><orgName type="division">Research Centre of Infection and Immunology, Faculty of Medicine</orgName><orgName type="institution">The University of Hong Kong</orgName><address><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation><affiliation><orgName type="division">State Key Laboratory of Emerging Infectious Diseases</orgName><orgName type="institution">The University of Hong Kong</orgName><address><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation></author><author xml:id="author-0003"><persName><forename type="first">Hoi‐wah</forename><surname>Tsoi</surname></persName><affiliation><orgName type="division">Department of Microbiology, The University of Hong Kong</orgName><orgName type="institution">University Pathology Building</orgName><address><street>Queen Mary Hospital</street><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation></author><author xml:id="author-0004" role="corresp"><persName><forename type="first">Kwok‐yung</forename><surname>Yuen</surname></persName><affiliation><orgName type="division">Department of Microbiology, The University of Hong Kong</orgName><orgName type="institution">University Pathology Building</orgName><address><street>Queen Mary Hospital</street><country key="HK" xml:lang="en">HONG KONG</country></address></affiliation><affiliation><orgName type="division">Research Centre of Infection and Immunology, Faculty 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type="book-part-DOI">10.1111/mim.2005.49.issue-10</idno><idno type="product">MIM</idno><imprint><biblScope unit="vol">49</biblScope><biblScope unit="issue">10</biblScope><biblScope unit="page" from="899">899</biblScope><biblScope unit="page" to="908">908</biblScope><biblScope unit="page-count">10</biblScope><date type="published" when="2005-10"></date></imprint></monogr></biblStruct></sourceDesc></fileDesc><encodingDesc><schemaRef type="ODD" url="https://xml-schema.delivery.istex.fr/tei-istex.odd"></schemaRef><appInfo><application ident="pub2tei" version="1.0.10" when="2019-12-20"><label>pub2TEI-ISTEX</label><desc>A set of style sheets for converting XML documents encoded in various scientific publisher formats into a common TEI format.
<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract style="main"><head>Abstract</head><p>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 <hi rend="italic">in silico</hi> 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 (3CL<hi rend="superscript">pro</hi>) into 16 polypeptides homologous to the corresponding polypeptides in other coronaviruses. Surprisingly, analysis of the putative cleavage sites of the 3CL<hi rend="superscript">pro</hi> revealed a unique putative cleavage site. In all known coronaviruses, the P1 positions at the cleavage sites of the 3CL<hi rend="superscript">pro</hi> 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 3CL<hi rend="superscript">pro</hi> will confirm the presence of this novel cleavage site.</p></abstract><textClass><keywords><term xml:id="mim03681-kwd-0001">coronavirus HKU1</term><term xml:id="mim03681-kwd-0002">ORF1ab</term><term xml:id="mim03681-kwd-0003">3C‐like protease</term></keywords><keywords rend="articleCategory"><term>Article</term></keywords><keywords rend="tocHeading1"><term>Articles</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-0NF3QX7S-2/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en" xml:id="MIM03681"><header><publicationMeta level="product"><doi origin="wiley">10.1111/(ISSN)1348-0421</doi><issn type="print">0385-5600</issn><issn type="electronic">1348-0421</issn><idGroup><id type="product" value="MIM"></id></idGroup><countGroup><count type="figureTotal" number="5"></count><count type="tableTotal" number="2"></count><count type="referenceTotal" number="56"></count></countGroup><titleGroup><title type="main" sort="MICROBIOLOGY AND IMMUNOLOGY">Microbiology and Immunology</title><title type="short">Microbiology and Immunology</title></titleGroup></publicationMeta><publicationMeta level="part" position="100"><doi origin="wiley">10.1111/mim.2005.49.issue-10</doi><copyright ownership="publisher">© owned by Center for Academic Publications Japan (Publisher)</copyright><numberingGroup><numbering type="journalVolume" number="49">49</numbering><numbering type="journalIssue">10</numbering></numberingGroup><coverDate startDate="2005-10">October 2005</coverDate></publicationMeta><publicationMeta level="unit" position="30" type="article" status="forIssue"><doi origin="wiley">10.1111/j.1348-0421.2005.tb03681.x</doi><idGroup><id type="unit" value="MIM03681"></id></idGroup><countGroup><count type="pageTotal" number="10"></count></countGroup><titleGroup><title type="articleCategory">Article</title><title type="tocHeading1">Articles</title></titleGroup><copyright ownership="thirdParty">© owned by Center for Academic Publications Japan (Publisher)</copyright><eventGroup><event type="manuscriptReceived" date="2005-03-23"></event><event type="manuscriptRevised" date="2005-07-12"></event><event type="manuscriptAccepted" date="2005-07-28"></event><event type="xmlCreated" agent="Aptara" date="2013-10-31"></event><event type="firstOnline" date="2013-11-14"></event><event type="publishedOnlineFinalForm" date="2013-11-14"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-31"></event></eventGroup><numberingGroup><numbering type="pageFirst">899</numbering><numbering type="pageLast">908</numbering></numberingGroup><correspondenceTo><i>Address correspondence to</i> Dr. Kwok‐yung Yuen, Department of Microbiology, The University of Hong Kong, Room 423 University Pathology Building, Queen Mary Hospital Compound, Pokfulam Road, Hong Kong. Fax: +852‐2855‐1241. E‐mail: <email>hkumicro@hkucc.hku.hk</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file://MIM.MIM03681.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main"><i>In Silico</i> Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease</title></titleGroup><creators><creator xml:id="mim03681-cr-0001" creatorRole="author" affiliationRef="#mim03681-aff-0001 #mim03681-aff-0002 #mim03681-aff-0003" noteRef="#mim03681-note-0001" corresponding="no"><personName><givenNames>Patrick C.Y.</givenNames><familyName>Woo</familyName></personName></creator><creator xml:id="mim03681-cr-0002" creatorRole="author" affiliationRef="#mim03681-aff-0001" noteRef="#mim03681-note-0001" corresponding="no"><personName><givenNames>Yi</givenNames><familyName>Huang</familyName></personName></creator><creator xml:id="mim03681-cr-0003" creatorRole="author" affiliationRef="#mim03681-aff-0001 #mim03681-aff-0002 #mim03681-aff-0003" corresponding="no"><personName><givenNames>Susanna K.P.</givenNames><familyName>Lau</familyName></personName></creator><creator xml:id="mim03681-cr-0004" creatorRole="author" affiliationRef="#mim03681-aff-0001" corresponding="no"><personName><givenNames>Hoi‐wah</givenNames><familyName>Tsoi</familyName></personName></creator><creator xml:id="mim03681-cr-0005" creatorRole="author" affiliationRef="#mim03681-aff-0001 #mim03681-aff-0002 #mim03681-aff-0003" corresponding="yes"><personName><givenNames>Kwok‐yung</givenNames><familyName>Yuen</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="mim03681-aff-0001" type="organization" countryCode="HK"><orgDiv>Department of Microbiology, The University of Hong Kong</orgDiv><orgName>University Pathology Building</orgName><address><street>Queen Mary Hospital</street><country>Hong Kong</country></address></affiliation><affiliation xml:id="mim03681-aff-0002" type="organization" countryCode="HK"><orgDiv>Research Centre of Infection and Immunology, Faculty of Medicine</orgDiv><orgName>The University of Hong Kong</orgName><address><country>Hong Kong</country></address></affiliation><affiliation xml:id="mim03681-aff-0003" type="organization" countryCode="HK"><orgDiv>State Key Laboratory of Emerging Infectious Diseases</orgDiv><orgName>The University of Hong Kong</orgName><address><country>Hong Kong</country></address></affiliation></affiliationGroup><keywordGroup type="author"><keyword xml:id="mim03681-kwd-0001">coronavirus HKU1</keyword><keyword xml:id="mim03681-kwd-0002">ORF1ab</keyword><keyword xml:id="mim03681-kwd-0003">3C‐like protease</keyword></keywordGroup><fundingInfo><fundingAgency>Research Grant Council</fundingAgency><fundingNumber>7616/05M</fundingNumber></fundingInfo><fundingInfo><fundingAgency>Health, Welfare and Food Bureau of the Hong Kong SAR Government</fundingAgency></fundingInfo><fundingInfo><fundingAgency>Suen Chi Sun Charitable Foundation</fundingAgency></fundingInfo><fundingInfo><fundingAgency>Infectious Diseases and William Benter Infectious Disease Fund</fundingAgency></fundingInfo><abstractGroup><abstract type="main"><title type="main">Abstract</title><p>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 <i>in silico</i> 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 (3CL<sup>pro</sup>) into 16 polypeptides homologous to the corresponding polypeptides in other coronaviruses. Surprisingly, analysis of the putative cleavage sites of the 3CL<sup>pro</sup> revealed a unique putative cleavage site. In all known coronaviruses, the P1 positions at the cleavage sites of the 3CL<sup>pro</sup> 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 3CL<sup>pro</sup> will confirm the presence of this novel cleavage site.</p></abstract></abstractGroup></contentMeta><noteGroup xml:id="mim03681-ntgp-0001"><note xml:id="mim03681-note-0001"><label>1</label> These authors contributed the same to the manuscript.</note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease</title></titleInfo><name type="personal"><namePart type="given">Patrick C.Y.</namePart><namePart type="family">Woo</namePart><affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</affiliation><affiliation>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</affiliation><affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</affiliation><description>These authors contributed the same to the manuscript.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Yi</namePart><namePart type="family">Huang</namePart><affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</affiliation><description>These authors contributed the same to the manuscript.</description><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Susanna K.P.</namePart><namePart type="family">Lau</namePart><affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</affiliation><affiliation>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</affiliation><affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hoi‐wah</namePart><namePart type="family">Tsoi</namePart><affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Kwok‐yung</namePart><namePart type="family">Yuen</namePart><affiliation>Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong</affiliation><affiliation>Research Centre of Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong</affiliation><affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</affiliation><affiliation>E-mail: hkumicro@hkucc.hku.hk</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><dateIssued encoding="w3cdtf">2005-10</dateIssued><dateCreated encoding="w3cdtf">2013-10-31</dateCreated><dateCaptured encoding="w3cdtf">2005-03-23</dateCaptured><dateValid encoding="w3cdtf">2005-07-28</dateValid><copyrightDate encoding="w3cdtf">2005</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><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.</abstract><note type="funding">Research Grant Council - No. 7616/05M; </note><note type="funding">Health, Welfare and Food Bureau of the Hong Kong SAR Government</note><note type="funding">Suen Chi Sun Charitable Foundation</note><note type="funding">Infectious Diseases and William Benter Infectious Disease Fund</note><subject><genre>keywords</genre><topic>coronavirus HKU1</topic><topic>ORF1ab</topic><topic>3C‐like protease</topic></subject><relatedItem type="host"><titleInfo><title>Microbiology and Immunology</title></titleInfo><titleInfo type="abbreviated"><title>Microbiology and Immunology</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>article-category</genre><topic>Article</topic><topic>Articles</topic></subject><identifier type="ISSN">0385-5600</identifier><identifier type="eISSN">1348-0421</identifier><identifier type="DOI">10.1111/(ISSN)1348-0421</identifier><identifier type="PublisherID">MIM</identifier><part><date>2005</date><detail type="volume"><caption>vol.</caption><number>49</number></detail><detail type="issue"><caption>no.</caption><number>10</number></detail><extent unit="pages"><start>899</start><end>908</end><total>10</total></extent></part></relatedItem><relatedItem type="references" displayLabel="mim03681-cit-0001"><titleInfo><title>Crystal structure of the RNA‐dependent RNA polymerase of hepatitis C virus</title></titleInfo><name type="personal"><namePart type="given">H.</namePart><namePart type="family">Ago</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">T.</namePart><namePart type="family">Adachi</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="family">Yoshida</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.</namePart><namePart type="family">Yamamoto</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">N.</namePart><namePart type="family">Habuka</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">K.</namePart><namePart type="family">Yatsunami</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.</namePart><namePart type="family">Miyano</namePart><role><roleTerm type="text">author</roleTerm></role></name><genre>journal-article</genre><note type="citation/reference">Ago, H., Adachi, T., Yoshida, A., Yamamoto, M., Habuka, N., Yatsunami, K., and Miyano, M. 1999. 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