Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases.
Identifieur interne : 000D13 ( PubMed/Corpus ); précédent : 000D12; suivant : 000D14Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases.
Auteurs : Mahmoud Kandeel ; Abdallah AltaherSource :
- Biological & pharmaceutical bulletin [ 1347-5215 ] ; 2017.
English descriptors
- KwdEn :
- Computational Biology (methods), Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (genetics), Evolution, Molecular, Genome, Viral, Middle East Respiratory Syndrome Coronavirus (enzymology), Middle East Respiratory Syndrome Coronavirus (genetics), Middle East Respiratory Syndrome Coronavirus (physiology), Papain (chemistry), Papain (genetics), Protein Processing, Post-Translational, Silent Mutation (genetics), Viral Proteins (chemistry), Viral Proteins (genetics), Virus Replication (genetics).
- MESH :
- chemical , chemistry : Cysteine Endopeptidases, Papain, Viral Proteins.
- chemical , genetics : Cysteine Endopeptidases, Papain, Viral Proteins.
- enzymology : Middle East Respiratory Syndrome Coronavirus.
- genetics : Middle East Respiratory Syndrome Coronavirus, Silent Mutation, Virus Replication.
- methods : Computational Biology.
- physiology : Middle East Respiratory Syndrome Coronavirus.
- Evolution, Molecular, Genome, Viral, Protein Processing, Post-Translational.
Abstract
Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro.
DOI: 10.1248/bpb.b17-00168
PubMed: 28420819
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pubmed:28420819Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases.</title><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation><nlm:affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</nlm:affiliation></affiliation></author><author><name sortKey="Altaher, Abdallah" sort="Altaher, Abdallah" uniqKey="Altaher A" first="Abdallah" last="Altaher">Abdallah Altaher</name><affiliation><nlm:affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28420819</idno><idno type="pmid">28420819</idno><idno type="doi">10.1248/bpb.b17-00168</idno><idno type="wicri:Area/PubMed/Corpus">000D13</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D13</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases.</title><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation><nlm:affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</nlm:affiliation></affiliation></author><author><name sortKey="Altaher, Abdallah" sort="Altaher, Abdallah" uniqKey="Altaher A" first="Abdallah" last="Altaher">Abdallah Altaher</name><affiliation><nlm:affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Biological & pharmaceutical bulletin</title><idno type="eISSN">1347-5215</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Cysteine Endopeptidases (chemistry)</term><term>Cysteine Endopeptidases (genetics)</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Middle East Respiratory Syndrome Coronavirus (enzymology)</term><term>Middle East Respiratory Syndrome Coronavirus (genetics)</term><term>Middle East Respiratory Syndrome Coronavirus (physiology)</term><term>Papain (chemistry)</term><term>Papain (genetics)</term><term>Protein Processing, Post-Translational</term><term>Silent Mutation (genetics)</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term><term>Virus Replication (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Papain</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Cysteine Endopeptidases</term><term>Papain</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>Silent Mutation</term><term>Virus Replication</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Protein Processing, Post-Translational</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28420819</PMID><DateCompleted><Year>2018</Year><Month>03</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>03</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1347-5215</ISSN><JournalIssue CitedMedium="Internet"><Volume>40</Volume><Issue>7</Issue><PubDate><Year>2017</Year><Month>Jul</Month><Day>01</Day></PubDate></JournalIssue><Title>Biological & pharmaceutical bulletin</Title><ISOAbbreviation>Biol. Pharm. Bull.</ISOAbbreviation></Journal><ArticleTitle>Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases.</ArticleTitle><Pagination><MedlinePgn>1086-1091</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1248/bpb.b17-00168</ELocationID><Abstract><AbstractText>Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kandeel</LastName><ForeName>Mahmoud</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Altaher</LastName><ForeName>Abdallah</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Japan</Country><MedlineTA>Biol Pharm Bull</MedlineTA><NlmUniqueID>9311984</NlmUniqueID><ISSNLinking>0918-6158</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.22.-</RegistryNumber><NameOfSubstance UI="D003546">Cysteine Endopeptidases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.22.2</RegistryNumber><NameOfSubstance UI="D010206">Papain</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.22.28</RegistryNumber><NameOfSubstance UI="C052731">3C proteases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003546" MajorTopicYN="N">Cysteine Endopeptidases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D065207" MajorTopicYN="N">Middle East Respiratory Syndrome Coronavirus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010206" MajorTopicYN="N">Papain</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011499" MajorTopicYN="N">Protein Processing, Post-Translational</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000069456" MajorTopicYN="N">Silent Mutation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014779" MajorTopicYN="N">Virus Replication</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">codon usage</Keyword><Keyword MajorTopicYN="N">coronavirus</Keyword><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">protease</Keyword><Keyword MajorTopicYN="N">synonymous codon</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>3</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28420819</ArticleId><ArticleId IdType="doi">10.1248/bpb.b17-00168</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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