Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse
Identifieur interne : 000178 ( Ncbi/Merge ); précédent : 000177; suivant : 000179Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse
Auteurs : Insung Ahn [Corée du Sud] ; Byeong-Jin Jeong [Corée du Sud] ; Hyeon Seok Son [Corée du Sud]Source :
- Experimental & Molecular Medicine [ 1226-3613 ] ; 2009.
Abstract
Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.
Url:
DOI: 10.3858/emm.2009.41.10.081
PubMed: 19561398
PubMed Central: 2772977
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In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Exp Mol Med</journal-id><journal-id journal-id-type="publisher-id">EMM</journal-id><journal-title-group><journal-title>Experimental & Molecular Medicine</journal-title></journal-title-group><issn pub-type="ppub">1226-3613</issn><issn pub-type="epub">2092-6413</issn><publisher><publisher-name>Korean Society of Medical Biochemistry and Molecular Biology</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19561398</article-id><article-id pub-id-type="pmc">2772977</article-id><article-id pub-id-type="doi">10.3858/emm.2009.41.10.081</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ahn</surname><given-names>Insung</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="author-notes" rid="FN1">*</xref></contrib><contrib contrib-type="author"><name><surname>Jeong</surname><given-names>Byeong-Jin</given-names></name><xref ref-type="aff" rid="A2">2</xref><xref ref-type="aff" rid="A3">3</xref><xref ref-type="author-notes" rid="FN1">*</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Son</surname><given-names>Hyeon Seok</given-names></name><xref ref-type="aff" rid="A2">2</xref><xref ref-type="aff" rid="A3">3</xref></contrib></contrib-group><aff id="A1"><label>1</label>Supercomputing Center, Korea Institute of Science and Technology Information, Daejon 305-806, Korea.</aff><aff id="A2"><label>2</label>Laboratory of Computational Biology and Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul 110-799, Korea.</aff><aff id="A3"><label>3</label>Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, Seoul 151-742, Korea.</aff><author-notes><corresp>Corresponding author: Tel, 82-2-740-8864; Fax, 82-2-762-9105; <email>hss2003@snu.ac.kr</email></corresp><fn id="FN1" fn-type="equal"><p><sup>*</sup>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="ppub"><day>31</day><month>10</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>30</day><month>10</month><year>2009</year></pub-date><volume>41</volume><issue>10</issue><fpage>746</fpage><lpage>756</lpage><history><date date-type="accepted"><day>16</day><month>6</month><year>2009</year></date></history><permissions><copyright-statement>Copyright © 2009 Korean Society of Medical Biochemistry and Molecular Biology</copyright-statement><copyright-year>2009</copyright-year></permissions><abstract><p>Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.</p></abstract><kwd-group><kwd>coronavirus</kwd><kwd>host-pathogen interactions</kwd><kwd>lectins, C-type</kwd></kwd-group></article-meta></front><floats-group><fig id="F1" position="float"><label>Figure 1</label><caption><p>Principal component analysis of the % GC contents on the 1<sup>st</sup>, 2<sup>nd</sup> and 3<sup>rd</sup> codon position. The first two factors from the principal component analysis (PRIN1 and PRIN2) were presented with each eigenvalue proportion. Nucleocapsid (A) and spike (B) coding genes of <italic>Coronavirus</italic> genus were compared with CTLD genes of human (<italic>homo sapiens</italic>) and mouse (<italic>mus musculus</italic>) species (C, D). Family names of CTLDs were also presented with each plot. G1, Group 1 CoV; G2, Group 2 CoV; G3, Group 3 CoV; N, nucleocapsid gene of CoV; S, spike gene of CoV; homo, <italic>homo sapiens</italic>; <italic>mus</italic>, <italic>mus musculus</italic>.</p></caption><graphic xlink:href="emm-41-746-g001"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><p>The results of phylogenetic analysis using the CTLD genes of human (<italic>homo sapiens</italic>) and mouse (<italic>mus musculus</italic>) species (A), and the scatter plots of the correspondence analysis using the relative synonymous codon usage values of the nucleocapsid and spike genes of CoVs as well as the CTLDs of human and mouse (B). Phylogram was derived by Neighbor-Joining method with bootstrap analysis of 1000 iterations, and bootstrap values (%) that are not 100% are represented as circulated numbers in each node. Each chromosome source of CTLD was also presented on the right column of tree. G1, Group 1 CoV; G2, Group 2 CoV; G3, Group 3 CoV; N, nucleocapsid gene of CoV; S, spike gene of CoV; CLEC, C-type lectin domain gene.</p></caption><graphic xlink:href="emm-41-746-g002"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><p>The profiles of the relative synonymous codon usage were shown as the vertical bar graph. The nucleocapaid (A) and spike (B) genes of human and mouse SARS-CoVs, as well as the human and mouse CTLD genes which were located near the nucleocapsid genes of SARS-CoVs (C) and were located far from those of SARS-CoVs (D) in the correspondence analysis in <xref ref-type="fig" rid="F2">Figure 2B</xref> are presented. Genbank accession numbers are presented in legends. G1, Group 1 CoV; G2, Group 2 CoV; G3, Group 3 CoV; N, nucleocapsid gene of CoV; S, spike gene of CoV; CLEC, C-type lectin domain gene.</p></caption><graphic xlink:href="emm-41-746-g003"></graphic></fig><table-wrap id="T1" position="float"><label>Table 1</label><caption><p>Eigenvectors and eigenvalues of the principal component analysis using the % GC contents on each codon position.</p></caption><graphic xlink:href="emm-41-746-i001"></graphic></table-wrap><table-wrap id="T2" position="float"><label>Table 2</label><caption><p>The results of the regression analysis between each dimensional factor of correspondence analysis using RSCU values of CoVs and each codon pattern parameters.</p></caption><graphic xlink:href="emm-41-746-i002"></graphic><table-wrap-foot><fn><p><sup>a</sup>First dimensional factor of the correspondence analysis, <sup>b</sup>Second dimensional factor of the correspondence analysis, <sup>c</sup>R<sup>2</sup> value of each linear regression analysis, <sup>d</sup>Parameter estimate which was resulted from linear regression analysis, <sup>e</sup>Effective number of codons. <sup>*</sup><italic>P</italic> < 0.0001.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc><affiliations><list><country><li>Corée du Sud</li></country><region><li>Région capitale de Séoul</li></region><settlement><li>Séoul</li></settlement><orgName><li>Université nationale de Séoul</li></orgName></list><tree><country name="Corée du Sud"><noRegion><name sortKey="Ahn, Insung" sort="Ahn, Insung" uniqKey="Ahn I" first="Insung" last="Ahn">Insung Ahn</name></noRegion><name sortKey="Jeong, Byeong Jin" sort="Jeong, Byeong Jin" uniqKey="Jeong B" first="Byeong-Jin" last="Jeong">Byeong-Jin Jeong</name><name sortKey="Jeong, Byeong Jin" sort="Jeong, Byeong Jin" uniqKey="Jeong B" first="Byeong-Jin" last="Jeong">Byeong-Jin Jeong</name><name sortKey="Son, Hyeon Seok" sort="Son, Hyeon Seok" uniqKey="Son H" first="Hyeon Seok" last="Son">Hyeon Seok Son</name><name sortKey="Son, Hyeon Seok" sort="Son, Hyeon Seok" uniqKey="Son H" first="Hyeon Seok" last="Son">Hyeon Seok Son</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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