Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum
Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic...
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| Veröffentlicht in: | Nucleic acids research 2006-09, Vol.34 (16), p.4583-4592 |
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| creator | Charles, Hubert Calevro, Federica Vinuelas, José Fayard, Jean-Michel Rahbe, Yvan |
| description | Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in BUCHNERA: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of BUCHNERA: |
| doi_str_mv | 10.1093/nar/gkl597 |
| format | Article |
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Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in BUCHNERA: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of BUCHNERA:</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkl597</identifier><identifier>PMID: 16963497</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford Publishing Limited (England)</publisher><subject>Acyrthosiphon pisum ; Animals ; Anticodon ; Aphids - microbiology ; Buchnera ; Buchnera - genetics ; Buchnera - metabolism ; Buchnera aphidicola ; Codon ; Cytosine - analysis ; Diet ; Ecology, environment ; Gene Expression Regulation, Bacterial ; Guanine - analysis ; Life Sciences ; Molecular Biology ; Oligonucleotide Array Sequence Analysis ; Phenylalanine - metabolism ; RNA, Transfer - genetics ; RNA, Transfer - metabolism ; Symbiosis ; Tyrosine - metabolism</subject><ispartof>Nucleic acids research, 2006-09, Vol.34 (16), p.4583-4592</ispartof><rights>Copyright Oxford University Press(England) Sep 2006</rights><rights>Attribution - NonCommercial</rights><rights>2006 The Author(s) 2006</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c492t-e6e8cb0d2d4aef686e4c302dd84716726a2b896c77bf0ac20a8ba5244e3babe53</citedby><cites>FETCH-LOGICAL-c492t-e6e8cb0d2d4aef686e4c302dd84716726a2b896c77bf0ac20a8ba5244e3babe53</cites><orcidid>0000-0002-0074-4443 ; 0000-0002-0809-4705 ; 0000-0001-7856-9617</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636365/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636365/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16963497$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-00391277$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Charles, Hubert</creatorcontrib><creatorcontrib>Calevro, Federica</creatorcontrib><creatorcontrib>Vinuelas, José</creatorcontrib><creatorcontrib>Fayard, Jean-Michel</creatorcontrib><creatorcontrib>Rahbe, Yvan</creatorcontrib><title>Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in BUCHNERA: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of BUCHNERA:</description><subject>Acyrthosiphon pisum</subject><subject>Animals</subject><subject>Anticodon</subject><subject>Aphids - microbiology</subject><subject>Buchnera</subject><subject>Buchnera - genetics</subject><subject>Buchnera - metabolism</subject><subject>Buchnera aphidicola</subject><subject>Codon</subject><subject>Cytosine - analysis</subject><subject>Diet</subject><subject>Ecology, environment</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Guanine - analysis</subject><subject>Life Sciences</subject><subject>Molecular Biology</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Phenylalanine - metabolism</subject><subject>RNA, Transfer - genetics</subject><subject>RNA, Transfer - metabolism</subject><subject>Symbiosis</subject><subject>Tyrosine - metabolism</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkl2L1TAQhoso7nH1xh-gwQtBoW6-mjY3wvGgrnBQUPc6TNP0NGvb1CQ9uD_C_2xKD37sjczFDJNn3gzDm2WPCX5FsGQXI_iLw7e-kOWdbEOYoDmXgt7NNpjhIieYV2fZgxCuMSacFPx-dkaEFIzLcpP93LnGjWgOcDCothAQjA2Knz9ukTsan5sfkzch2MTYEb2ZdTcaDwimzjZWuz6VbTQegXcDRKsRDHZ0CLRt0DhHb2MahR6FuMigRSYG1LkQ0Vbf-JgqO3WpPdkwDw-zey30wTw65fPs6t3br7vLfP_p_Yfddp9rLmnMjTCVrnFDGw6mFZUwXDNMm6biJRElFUDrSgpdlnWLQVMMVQ0F5dywGmpTsPPs9ao7zfVgGm3G6KFXk7cD-BvlwKp_X0bbqYM7KiJYikXgxSrQ3Rq73O7V0sOYSULL8kgS-_z0mXffZxOiGmzQpu9hNG4OSlSywAX-P0gkE1iSBXx2C7x2s09nDopiLHDJyipBL1dIexeCN-3vPQlWi29U8o1afZPgJ38f5A96MkoCnq5AC07Bwdugrr7QtDQmBFekqNgvXCrLSg</recordid><startdate>20060901</startdate><enddate>20060901</enddate><creator>Charles, Hubert</creator><creator>Calevro, Federica</creator><creator>Vinuelas, José</creator><creator>Fayard, Jean-Michel</creator><creator>Rahbe, Yvan</creator><general>Oxford Publishing Limited (England)</general><general>Oxford University Press</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-0074-4443</orcidid><orcidid>https://orcid.org/0000-0002-0809-4705</orcidid><orcidid>https://orcid.org/0000-0001-7856-9617</orcidid></search><sort><creationdate>20060901</creationdate><title>Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum</title><author>Charles, Hubert ; Calevro, Federica ; Vinuelas, José ; Fayard, Jean-Michel ; Rahbe, Yvan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c492t-e6e8cb0d2d4aef686e4c302dd84716726a2b896c77bf0ac20a8ba5244e3babe53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Acyrthosiphon pisum</topic><topic>Animals</topic><topic>Anticodon</topic><topic>Aphids - microbiology</topic><topic>Buchnera</topic><topic>Buchnera - genetics</topic><topic>Buchnera - metabolism</topic><topic>Buchnera aphidicola</topic><topic>Codon</topic><topic>Cytosine - analysis</topic><topic>Diet</topic><topic>Ecology, environment</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Guanine - analysis</topic><topic>Life Sciences</topic><topic>Molecular Biology</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Phenylalanine - metabolism</topic><topic>RNA, Transfer - genetics</topic><topic>RNA, Transfer - metabolism</topic><topic>Symbiosis</topic><topic>Tyrosine - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Charles, Hubert</creatorcontrib><creatorcontrib>Calevro, Federica</creatorcontrib><creatorcontrib>Vinuelas, José</creatorcontrib><creatorcontrib>Fayard, Jean-Michel</creatorcontrib><creatorcontrib>Rahbe, Yvan</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Charles, Hubert</au><au>Calevro, Federica</au><au>Vinuelas, José</au><au>Fayard, Jean-Michel</au><au>Rahbe, Yvan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2006-09-01</date><risdate>2006</risdate><volume>34</volume><issue>16</issue><spage>4583</spage><epage>4592</epage><pages>4583-4592</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in BUCHNERA: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of BUCHNERA:</abstract><cop>England</cop><pub>Oxford Publishing Limited (England)</pub><pmid>16963497</pmid><doi>10.1093/nar/gkl597</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0002-0074-4443</orcidid><orcidid>https://orcid.org/0000-0002-0809-4705</orcidid><orcidid>https://orcid.org/0000-0001-7856-9617</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Acyrthosiphon pisum Animals Anticodon Aphids - microbiology Buchnera Buchnera - genetics Buchnera - metabolism Buchnera aphidicola Codon Cytosine - analysis Diet Ecology, environment Gene Expression Regulation, Bacterial Guanine - analysis Life Sciences Molecular Biology Oligonucleotide Array Sequence Analysis Phenylalanine - metabolism RNA, Transfer - genetics RNA, Transfer - metabolism Symbiosis Tyrosine - metabolism |
| title | Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum |
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