Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System
Identifieur interne : 000A90 ( Pmc/Curation ); précédent : 000A89; suivant : 000A91Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System
Auteurs : Benjamin D. Greenbaum [États-Unis] ; Raul Rabadan [États-Unis] ; Arnold J. Levine [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2009.
Abstract
The innate immune response provides a first line of defense against pathogens by targeting generic differential features that are present in foreign organisms but not in the host. These innate responses generate selection forces acting both in pathogens and hosts that further determine their co-evolution. Here we analyze the nucleic acid sequence fingerprints of these selection forces acting in parallel on both host innate immune genes and ssRNA viral genomes. We do this by identifying dinucleotide biases in the coding regions of innate immune response genes in plasmacytoid dendritic cells, and then use this signal to identify other significant host innate immune genes. The persistence of these biases in the orthologous groups of genes in humans and chickens is also examined. We then compare the significant motifs in highly expressed genes of the innate immune system to those in ssRNA viruses and study the evolution of these motifs in the H1N1 influenza genome. We argue that the significant under-represented motif pattern of CpG in an AU context - which is found in both the ssRNA viruses and innate genes, and has decreased throughout the history of H1N1 influenza replication in humans - is immunostimulatory and has been selected against during the co-evolution of viruses and host innate immune genes. This shows how differences in host immune biology can drive the evolution of viruses that jump into species with different immune priorities than the original host.
Url:
DOI: 10.1371/journal.pone.0005969
PubMed: 19536338
PubMed Central: 2694999
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<front><div type="abstract" xml:lang="en"><p>The innate immune response provides a first line of defense against pathogens by targeting generic differential features that are present in foreign organisms but not in the host. These innate responses generate selection forces acting both in pathogens and hosts that further determine their co-evolution. Here we analyze the nucleic acid sequence fingerprints of these selection forces acting in parallel on both host innate immune genes and ssRNA viral genomes. We do this by identifying dinucleotide biases in the coding regions of innate immune response genes in plasmacytoid dendritic cells, and then use this signal to identify other significant host innate immune genes. The persistence of these biases in the orthologous groups of genes in humans and chickens is also examined. We then compare the significant motifs in highly expressed genes of the innate immune system to those in ssRNA viruses and study the evolution of these motifs in the H1N1 influenza genome. We argue that the significant under-represented motif pattern of CpG in an AU context - which is found in both the ssRNA viruses and innate genes, and has decreased throughout the history of H1N1 influenza replication in humans - is immunostimulatory and has been selected against during the co-evolution of viruses and host innate immune genes. This shows how differences in host immune biology can drive the evolution of viruses that jump into species with different immune priorities than the original host.</p>
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</author>
<author><name sortKey="Travers, P" uniqKey="Travers P">P Travers</name>
</author>
<author><name sortKey="Walport, M" uniqKey="Walport M">M Walport</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Akira, S" uniqKey="Akira S">S Akira</name>
</author>
<author><name sortKey="Uematsu, S" uniqKey="Uematsu S">S Uematsu</name>
</author>
<author><name sortKey="Takeuchi, O" uniqKey="Takeuchi O">O Takeuchi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hongbo, C" uniqKey="Hongbo C">C Hongbo</name>
</author>
<author><name sortKey="Flavell, Ra" uniqKey="Flavell R">RA Flavell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Greenbaum, Bd" uniqKey="Greenbaum B">BD Greenbaum</name>
</author>
<author><name sortKey="Levine, Aj" uniqKey="Levine A">AJ Levine</name>
</author>
<author><name sortKey="Bhanot, G" uniqKey="Bhanot G">G Bhanot</name>
</author>
<author><name sortKey="Rabadan, R" uniqKey="Rabadan R">R Rabadan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hemmi, H" uniqKey="Hemmi H">H Hemmi</name>
</author>
<author><name sortKey="Takeuchi, O" uniqKey="Takeuchi O">O Takeuchi</name>
</author>
<author><name sortKey="Kawai, T" uniqKey="Kawai T">T Kawai</name>
</author>
<author><name sortKey="Kaisho, T" uniqKey="Kaisho T">T Kaisho</name>
</author>
<author><name sortKey="Sato, S" uniqKey="Sato S">S Sato</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lund, Jm" uniqKey="Lund J">JM Lund</name>
</author>
<author><name sortKey="Alexopoulou, L" uniqKey="Alexopoulou L">L Alexopoulou</name>
</author>
<author><name sortKey="Sato, A" uniqKey="Sato A">A Sato</name>
</author>
<author><name sortKey="Karow, M" uniqKey="Karow M">M Karow</name>
</author>
<author><name sortKey="Adams, Nc" uniqKey="Adams N">NC Adams</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heil, F" uniqKey="Heil F">F Heil</name>
</author>
<author><name sortKey="Hemmi, H" uniqKey="Hemmi H">H Hemmi</name>
</author>
<author><name sortKey="Hocherin, H" uniqKey="Hocherin H">H Hocherin</name>
</author>
<author><name sortKey="Ampenberger, F" uniqKey="Ampenberger F">F Ampenberger</name>
</author>
<author><name sortKey="Kirschnining, C" uniqKey="Kirschnining C">C Kirschnining</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Akira, S" uniqKey="Akira S">S Akira</name>
</author>
<author><name sortKey="Sato, S" uniqKey="Sato S">S Sato</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sugiyama, T" uniqKey="Sugiyama T">T Sugiyama</name>
</author>
<author><name sortKey="Gursel, M" uniqKey="Gursel M">M Gursel</name>
</author>
<author><name sortKey="Takeshita, F" uniqKey="Takeshita F">F Takeshita</name>
</author>
<author><name sortKey="Coban, C" uniqKey="Coban C">C Coban</name>
</author>
<author><name sortKey="Conover, J" uniqKey="Conover J">J Conover</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="O Doherty, U" uniqKey="O Doherty U">U O'Doherty</name>
</author>
<author><name sortKey="Peng, M" uniqKey="Peng M">M Peng</name>
</author>
<author><name sortKey="Gezelter, S" uniqKey="Gezelter S">S Gezelter</name>
</author>
<author><name sortKey="Swiggard, Wj" uniqKey="Swiggard W">WJ Swiggard</name>
</author>
<author><name sortKey="Betjes, M" uniqKey="Betjes M">M Betjes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grouard, G" uniqKey="Grouard G">G Grouard</name>
</author>
<author><name sortKey="Rissoan, Mc" uniqKey="Rissoan M">MC Rissoan</name>
</author>
<author><name sortKey="Filgueira, L" uniqKey="Filgueira L">L Filgueira</name>
</author>
<author><name sortKey="Durand, I" uniqKey="Durand I">I Durand</name>
</author>
<author><name sortKey="Banchereau, J" uniqKey="Banchereau J">J Banchereau</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rothenfusser, S" uniqKey="Rothenfusser S">S Rothenfusser</name>
</author>
<author><name sortKey="Tuma, E" uniqKey="Tuma E">E Tuma</name>
</author>
<author><name sortKey="Endres, S" uniqKey="Endres S">S Endres</name>
</author>
<author><name sortKey="Hartman, G" uniqKey="Hartman G">G Hartman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mckenna, K" uniqKey="Mckenna K">K McKenna</name>
</author>
<author><name sortKey="Beignon, A" uniqKey="Beignon A">A Beignon</name>
</author>
<author><name sortKey="Bhardwaj, N" uniqKey="Bhardwaj N">N Bhardwaj</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Colonna, M" uniqKey="Colonna M">M Colonna</name>
</author>
<author><name sortKey="Trinchieri, G" uniqKey="Trinchieri G">G Trinchieri</name>
</author>
<author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Theofilopoulos, An" uniqKey="Theofilopoulos A">AN Theofilopoulos</name>
</author>
<author><name sortKey="Baccala, R" uniqKey="Baccala R">R Baccala</name>
</author>
<author><name sortKey="Beutler, B" uniqKey="Beutler B">B Beutler</name>
</author>
<author><name sortKey="Kono, Dh" uniqKey="Kono D">DH Kono</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marshak Rothstein, A" uniqKey="Marshak Rothstein A">A Marshak-Rothstein</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kreig, Am" uniqKey="Kreig A">AM Kreig</name>
</author>
<author><name sortKey="Vollmer, J" uniqKey="Vollmer J">J Vollmer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lowy, Rj" uniqKey="Lowy R">RJ Lowy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Iparraguirre, A" uniqKey="Iparraguirre A">A Iparraguirre</name>
</author>
<author><name sortKey="Tobias, Jw" uniqKey="Tobias J">JW Tobias</name>
</author>
<author><name sortKey="Hensley, Se" uniqKey="Hensley S">SE Hensley</name>
</author>
<author><name sortKey="Masek, Ks" uniqKey="Masek K">KS Masek</name>
</author>
<author><name sortKey="Cavanagh, Ll" uniqKey="Cavanagh L">LL Cavanagh</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Karolchik, D" uniqKey="Karolchik D">D Karolchik</name>
</author>
<author><name sortKey="Baertsch, R" uniqKey="Baertsch R">R Baertsch</name>
</author>
<author><name sortKey="Diekhans, M" uniqKey="Diekhans M">M Diekhans</name>
</author>
<author><name sortKey="Furey, Ts" uniqKey="Furey T">TS Furey</name>
</author>
<author><name sortKey="Hinrichs, A" uniqKey="Hinrichs A">A Hinrichs</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karolchik, D" uniqKey="Karolchik D">D Karolchik</name>
</author>
<author><name sortKey="Baertsch, R" uniqKey="Baertsch R">R Baertsch</name>
</author>
<author><name sortKey="Diekhans, M" uniqKey="Diekhans M">M Diekhans</name>
</author>
<author><name sortKey="Furey, Ts" uniqKey="Furey T">TS Furey</name>
</author>
<author><name sortKey="Hinrichs, A" uniqKey="Hinrichs A">A Hinrichs</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Burge, C" uniqKey="Burge C">C Burge</name>
</author>
<author><name sortKey="Campbell, Am" uniqKey="Campbell A">AM Campbell</name>
</author>
<author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name>
</author>
<author><name sortKey="Cardon, Lr" uniqKey="Cardon L">LR Cardon</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nakajima, K" uniqKey="Nakajima K">K Nakajima</name>
</author>
<author><name sortKey="Desselberger, U" uniqKey="Desselberger U">U Desselberger</name>
</author>
<author><name sortKey="Palese, P" uniqKey="Palese P">P Palese</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Raz, E" uniqKey="Raz E">E Raz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kobasa, D" uniqKey="Kobasa D">D Kobasa</name>
</author>
<author><name sortKey="Jones, Sm" uniqKey="Jones S">SM Jones</name>
</author>
<author><name sortKey="Shinya, K" uniqKey="Shinya K">K Shinya</name>
</author>
<author><name sortKey="Kash, Jc" uniqKey="Kash J">JC Kash</name>
</author>
<author><name sortKey="Copps, J" uniqKey="Copps J">J Copps</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Watanabe, T" uniqKey="Watanabe T">T Watanabe</name>
</author>
<author><name sortKey="Watanabe, S" uniqKey="Watanabe S">S Watanabe</name>
</author>
<author><name sortKey="Shinya, K" uniqKey="Shinya K">K Shinya</name>
</author>
<author><name sortKey="Kim, Jh" uniqKey="Kim J">JH Kim</name>
</author>
<author><name sortKey="Hatta, M" uniqKey="Hatta M">M Hatta</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Salser, W" uniqKey="Salser W">W Salser</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nussinov, R" uniqKey="Nussinov R">R Nussinov</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jabbari, K" uniqKey="Jabbari K">K Jabbari</name>
</author>
<author><name sortKey="Bernardi, G" uniqKey="Bernardi G">G Bernardi</name>
</author>
</analytic>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">19536338</article-id>
<article-id pub-id-type="pmc">2694999</article-id>
<article-id pub-id-type="publisher-id">09-PONE-RA-09158R1</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0005969</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline"><subject>Immunology</subject>
<subject>Computational Biology/Genomics</subject>
<subject>Computational Biology/Sequence Motif Analysis</subject>
<subject>Computational Biology/Systems Biology</subject>
<subject>Immunology/Autoimmunity</subject>
<subject>Immunology/Cellular Microbiology and Pathogenesis</subject>
<subject>Immunology/Genetics of the Immune System</subject>
<subject>Immunology/Immune Response</subject>
<subject>Immunology/Innate Immunity</subject>
<subject>Mathematics/Statistics</subject>
<subject>Virology/Effects of Virus Infection on Host Gene Expression</subject>
<subject>Virology/Emerging Viral Diseases</subject>
<subject>Virology/Host Antiviral Responses</subject>
<subject>Virology/Immune Evasion</subject>
<subject>Infectious Diseases/Viral Infections</subject>
</subj-group>
</article-categories>
<title-group><article-title>Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System</article-title>
<alt-title alt-title-type="running-head">Oligo- Mediators RNA Innate</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Greenbaum</surname>
<given-names>Benjamin D.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rabadan</surname>
<given-names>Raul</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Levine</surname>
<given-names>Arnold J.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Institute for Advanced Study, Princeton, New Jersey, United States of America</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University College of Physicians and Surgeons, New York, New York, United States of America</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Seoighe</surname>
<given-names>Cathal</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">National University of Ireland Galway, Ireland</aff>
<author-notes><corresp id="cor1">* E-mail: <email>beng@ias.edu</email>
</corresp>
<fn fn-type="con"><p>Analyzed the data: BG RR AL. Contributed reagents/materials/analysis tools: BG RR. Wrote the paper: BG.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>18</day>
<month>6</month>
<year>2009</year>
</pub-date>
<volume>4</volume>
<issue>6</issue>
<elocation-id>e5969</elocation-id>
<history><date date-type="received"><day>11</day>
<month>3</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>24</day>
<month>4</month>
<year>2009</year>
</date>
</history>
<permissions><copyright-statement>Greenbaum et al.</copyright-statement>
<copyright-year>2009</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p>
</license>
</permissions>
<abstract><p>The innate immune response provides a first line of defense against pathogens by targeting generic differential features that are present in foreign organisms but not in the host. These innate responses generate selection forces acting both in pathogens and hosts that further determine their co-evolution. Here we analyze the nucleic acid sequence fingerprints of these selection forces acting in parallel on both host innate immune genes and ssRNA viral genomes. We do this by identifying dinucleotide biases in the coding regions of innate immune response genes in plasmacytoid dendritic cells, and then use this signal to identify other significant host innate immune genes. The persistence of these biases in the orthologous groups of genes in humans and chickens is also examined. We then compare the significant motifs in highly expressed genes of the innate immune system to those in ssRNA viruses and study the evolution of these motifs in the H1N1 influenza genome. We argue that the significant under-represented motif pattern of CpG in an AU context - which is found in both the ssRNA viruses and innate genes, and has decreased throughout the history of H1N1 influenza replication in humans - is immunostimulatory and has been selected against during the co-evolution of viruses and host innate immune genes. This shows how differences in host immune biology can drive the evolution of viruses that jump into species with different immune priorities than the original host.</p>
</abstract>
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</counts>
</article-meta>
</front>
</pmc>
</record>
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