Phylogenetic and molecular analysis of the ribulose-1,5-bisphosphate carboxylase small subunit gene family in banana
Identifieur interne : 001842 ( Istex/Corpus ); précédent : 001841; suivant : 001843Phylogenetic and molecular analysis of the ribulose-1,5-bisphosphate carboxylase small subunit gene family in banana
Auteurs : Skye Thomas-Hall ; Paul R. Campbell ; Katrien Carlens ; Emi Kawanishi ; Rony Swennen ; Lszl Sgi ; Peer M. SchenkSource :
- Journal of Experimental Botany [ 0022-0957 ] ; 2007-06-21.
Abstract
Despite being the number one fruit crop in the world, very little is known about the phylogeny and molecular biology of banana (Musa spp.). Six banana rbcS gene families encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from six different Musa spp. are presented. For a comprehensive phylogenetic study using Musa rbcS genes, a total of 57 distinct rbcS sequences was isolated from six accessions that contained different combinations of the A and B ancestral/parental genomes. As a result, five of the six members of the rbcS gene family could be affiliated with the A and/or B Musa genomes and at least three of the six gene families most likely existed before Musa A and B genomes separated. By combining sequence data with quantitative real-time PCR it was determined that the different Musa rbcS gene family members are also often multiply represented in each genome, with the highest copy numbers in the B genome. Expression of some of the rbcS genes varied in intensity and in different tissues indicating differences in regulation. To analyse and compare regulatory sequences of Musa rbcS genes, promoter and terminator regions were cloned for three Musa rbcS genes. Transient transformation assays using promoterreporterterminator constructs in maize, wheat, and sugarcane demonstrated that the rbcS-Ma1, rbcS-Ma3, and rbcS-Ma5 promoters could be useful for transgene expression in heterologous expression systems. Furthermore, the rbcS-Ma1 terminator resulted in a 2-fold increase of transgene expression when directly compared with the widely used Nos terminator.
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DOI: 10.1093/jxb/erm129
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Schenk</name><affiliation><mods:affiliation>School of Integrative Biology, The University of Queensland, St Lucia, Queensland 4072, Australia</mods:affiliation></affiliation><affiliation><mods:affiliation>Cooperative Research Centre for Tropical Plant Protection, The University of Queensland, St Lucia, Queensland 4072, Australia</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: p.schenk@uq.edu.au</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Experimental Botany</title><idno type="ISSN">0022-0957</idno><idno type="eISSN">1460-2431</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2007-06-21">2007-06-21</date><biblScope unit="volume">58</biblScope><biblScope unit="issue">10</biblScope><biblScope unit="page" from="2685">2685</biblScope><biblScope unit="page" to="2697">2697</biblScope></imprint><idno type="ISSN">0022-0957</idno></series><idno type="istex">17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA</idno><idno type="DOI">10.1093/jxb/erm129</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0022-0957</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Despite being the number one fruit crop in the world, very little is known about the phylogeny and molecular biology of banana (Musa spp.). Six banana rbcS gene families encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from six different Musa spp. are presented. For a comprehensive phylogenetic study using Musa rbcS genes, a total of 57 distinct rbcS sequences was isolated from six accessions that contained different combinations of the A and B ancestral/parental genomes. As a result, five of the six members of the rbcS gene family could be affiliated with the A and/or B Musa genomes and at least three of the six gene families most likely existed before Musa A and B genomes separated. By combining sequence data with quantitative real-time PCR it was determined that the different Musa rbcS gene family members are also often multiply represented in each genome, with the highest copy numbers in the B genome. Expression of some of the rbcS genes varied in intensity and in different tissues indicating differences in regulation. To analyse and compare regulatory sequences of Musa rbcS genes, promoter and terminator regions were cloned for three Musa rbcS genes. Transient transformation assays using promoterreporterterminator constructs in maize, wheat, and sugarcane demonstrated that the rbcS-Ma1, rbcS-Ma3, and rbcS-Ma5 promoters could be useful for transgene expression in heterologous expression systems. Furthermore, the rbcS-Ma1 terminator resulted in a 2-fold increase of transgene expression when directly compared with the widely used Nos terminator.</div></front></TEI><istex><corpusName>oup</corpusName><author><json:item><name>Skye Thomas-Hall</name><affiliations><json:string>School of Integrative Biology, The University of Queensland, St Lucia, Queensland 4072, Australia</json:string></affiliations></json:item><json:item><name>Paul R. 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Six banana rbcS gene families encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from six different Musa spp. are presented. For a comprehensive phylogenetic study using Musa rbcS genes, a total of 57 distinct rbcS sequences was isolated from six accessions that contained different combinations of the A and B ancestral/parental genomes. As a result, five of the six members of the rbcS gene family could be affiliated with the A and/or B Musa genomes and at least three of the six gene families most likely existed before Musa A and B genomes separated. By combining sequence data with quantitative real-time PCR it was determined that the different Musa rbcS gene family members are also often multiply represented in each genome, with the highest copy numbers in the B genome. Expression of some of the rbcS genes varied in intensity and in different tissues indicating differences in regulation. To analyse and compare regulatory sequences of Musa rbcS genes, promoter and terminator regions were cloned for three Musa rbcS genes. Transient transformation assays using promoterreporterterminator constructs in maize, wheat, and sugarcane demonstrated that the rbcS-Ma1, rbcS-Ma3, and rbcS-Ma5 promoters could be useful for transgene expression in heterologous expression systems. 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Six banana rbcS gene families encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from six different Musa spp. are presented. For a comprehensive phylogenetic study using Musa rbcS genes, a total of 57 distinct rbcS sequences was isolated from six accessions that contained different combinations of the A and B ancestral/parental genomes. As a result, five of the six members of the rbcS gene family could be affiliated with the A and/or B Musa genomes and at least three of the six gene families most likely existed before Musa A and B genomes separated. By combining sequence data with quantitative real-time PCR it was determined that the different Musa rbcS gene family members are also often multiply represented in each genome, with the highest copy numbers in the B genome. Expression of some of the rbcS genes varied in intensity and in different tissues indicating differences in regulation. To analyse and compare regulatory sequences of Musa rbcS genes, promoter and terminator regions were cloned for three Musa rbcS genes. Transient transformation assays using promoterreporterterminator constructs in maize, wheat, and sugarcane demonstrated that the rbcS-Ma1, rbcS-Ma3, and rbcS-Ma5 promoters could be useful for transgene expression in heterologous expression systems. Furthermore, the rbcS-Ma1 terminator resulted in a 2-fold increase of transgene expression when directly compared with the widely used Nos terminator.</p></abstract><textClass><keywords scheme="keyword"><list><item><term>Research Papers</term></item></list></keywords></textClass><textClass><keywords scheme="keyword"><list><head>keywords</head><item><term>Gene expression</term></item><item><term>intron</term></item><item><term>Musa</term></item><item><term>phylogenomic analysis</term></item><item><term>promoter</term></item><item><term>rbcS</term></item><item><term>RuBisCo</term></item><item><term>terminator</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2007-06-21">Created</change><change when="2007-06-21">Published</change><change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-10-14">References added</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus oup" wicri:toSee="no header"><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType><istex:document><article article-type="research-article"><front><journal-meta><journal-id journal-id-type="hwp">jexbot</journal-id><journal-id journal-id-type="publisher-id">exbotj</journal-id><journal-title>Journal of Experimental Botany</journal-title><issn pub-type="epub">1460-2431</issn><issn pub-type="ppub">0022-0957</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.1093/jxb/erm129</article-id><article-categories><subj-group><subject>Research Papers</subject></subj-group></article-categories><title-group><article-title>Phylogenetic and molecular analysis of the ribulose-1,5-bisphosphate carboxylase small subunit gene family in banana</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Thomas-Hall</surname><given-names>Skye</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Campbell</surname><given-names>Paul R.</given-names></name><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Carlens</surname><given-names>Katrien</given-names></name><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Kawanishi</surname><given-names>Emi</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Swennen</surname><given-names>Rony</given-names></name><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Sági</surname><given-names>László</given-names></name><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Schenk</surname><given-names>Peer M.</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="aff1"><label>1</label>School of Integrative Biology, The University of Queensland, St Lucia, Queensland 4072, Australia</aff><aff id="aff2"><label>2</label>Cooperative Research Centre for Tropical Plant Protection, The University of Queensland, St Lucia, Queensland 4072, Australia</aff><aff id="aff3"><label>3</label>Katholieke Universiteit Leuven, Laboratory of Tropical Crop Improvement, Kasteelpark Arenberg, 3001 Heverlee-Leuven, Belgium</aff><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed. E-mail: <email>p.schenk@uq.edu.au</email></corresp></author-notes><pub-date pub-type="epub-ppub"><month>7</month><year>2007</year></pub-date><pub-date pub-type="epub"><day>21</day><month>6</month><year>2007</year></pub-date><volume>58</volume><issue>10</issue><fpage>2685</fpage><lpage>2697</lpage><history><date date-type="received"><day>27</day><month>3</month><year>2007</year></date><date date-type="rev-recd"><day>17</day><month>5</month><year>2007</year></date><date date-type="accepted"><day>17</day><month>5</month><year>2007</year></date></history><permissions><copyright-statement>© 2007 The Author(s).</copyright-statement><copyright-year>2007</copyright-year><license license-type="open-access"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</p><p>This paper is available online free of all access charges (see <ext-link ext-link-type="uri" xlink:href="http://jxb.oxfordjournals.org/open_access.html">http://jxb.oxfordjournals.org/open_access.html</ext-link> for further details)</p></license></permissions><abstract><p>Despite being the number one fruit crop in the world, very little is known about the phylogeny and molecular biology of banana (<italic>Musa</italic> spp.). Six banana <italic>rbcS</italic> gene families encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from six different <italic>Musa</italic> spp. are presented. For a comprehensive phylogenetic study using <italic>Musa rbcS</italic> genes, a total of 57 distinct <italic>rbcS</italic> sequences was isolated from six accessions that contained different combinations of the A and B ancestral/parental genomes. As a result, five of the six members of the <italic>rbcS</italic> gene family could be affiliated with the A and/or B <italic>Musa</italic> genomes and at least three of the six gene families most likely existed before <italic>Musa</italic> A and B genomes separated. By combining sequence data with quantitative real-time PCR it was determined that the different <italic>Musa rbcS</italic> gene family members are also often multiply represented in each genome, with the highest copy numbers in the B genome. Expression of some of the <italic>rbcS</italic> genes varied in intensity and in different tissues indicating differences in regulation. To analyse and compare regulatory sequences of <italic>Musa rbcS</italic> genes, promoter and terminator regions were cloned for three <italic>Musa rbcS</italic> genes. Transient transformation assays using promoter–reporter–terminator constructs in maize, wheat, and sugarcane demonstrated that the <italic>rbcS-Ma1</italic>, <italic>rbcS-Ma3</italic>, and <italic>rbcS-Ma5</italic> promoters could be useful for transgene expression in heterologous expression systems. Furthermore, the <italic>rbcS-Ma1</italic> terminator resulted in a 2-fold increase of transgene expression when directly compared with the widely used <italic>Nos</italic> terminator.</p></abstract><kwd-group><kwd>Gene expression</kwd><kwd>intron</kwd><kwd>Musa</kwd><kwd>phylogenomic analysis</kwd><kwd>promoter</kwd><kwd>rbcS</kwd><kwd>RuBisCo</kwd><kwd>terminator</kwd></kwd-group></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>Phylogenetic and molecular analysis of the ribulose-1,5-bisphosphate carboxylase small subunit gene family in banana</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Phylogenetic and molecular analysis of the ribulose-1,5-bisphosphate carboxylase small subunit gene family in banana</title></titleInfo><name type="personal"><namePart type="given">Skye</namePart><namePart type="family">Thomas-Hall</namePart><affiliation>School of Integrative Biology, The University of Queensland, St Lucia, Queensland 4072, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Paul R.</namePart><namePart type="family">Campbell</namePart><affiliation>Cooperative Research Centre for Tropical Plant Protection, The University of Queensland, St Lucia, Queensland 4072, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Katrien</namePart><namePart type="family">Carlens</namePart><affiliation>Cooperative Research Centre for Tropical Plant Protection, The University of Queensland, St Lucia, Queensland 4072, Australia</affiliation><affiliation>Katholieke Universiteit Leuven, Laboratory of Tropical Crop Improvement, Kasteelpark Arenberg, 3001 Heverlee-Leuven, Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Emi</namePart><namePart type="family">Kawanishi</namePart><affiliation>School of Integrative Biology, The University of Queensland, St Lucia, Queensland 4072, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Rony</namePart><namePart type="family">Swennen</namePart><affiliation>Katholieke Universiteit Leuven, Laboratory of Tropical Crop Improvement, Kasteelpark Arenberg, 3001 Heverlee-Leuven, Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Lszl</namePart><namePart type="family">Sgi</namePart><affiliation>Katholieke Universiteit Leuven, Laboratory of Tropical Crop Improvement, Kasteelpark Arenberg, 3001 Heverlee-Leuven, Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal" displayLabel="corresp"><namePart type="given">Peer M.</namePart><namePart type="family">Schenk</namePart><affiliation>School of Integrative Biology, The University of Queensland, St Lucia, Queensland 4072, Australia</affiliation><affiliation>Cooperative Research Centre for Tropical Plant Protection, The University of Queensland, St Lucia, Queensland 4072, Australia</affiliation><affiliation>E-mail: p.schenk@uq.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="research-article"></genre><subject><topic>Research Papers</topic></subject><originInfo><publisher>Oxford University Press</publisher><dateIssued encoding="w3cdtf">2007-06-21</dateIssued><dateCreated encoding="w3cdtf">2007-06-21</dateCreated><copyrightDate encoding="w3cdtf">2007</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract>Despite being the number one fruit crop in the world, very little is known about the phylogeny and molecular biology of banana (Musa spp.). Six banana rbcS gene families encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from six different Musa spp. are presented. For a comprehensive phylogenetic study using Musa rbcS genes, a total of 57 distinct rbcS sequences was isolated from six accessions that contained different combinations of the A and B ancestral/parental genomes. As a result, five of the six members of the rbcS gene family could be affiliated with the A and/or B Musa genomes and at least three of the six gene families most likely existed before Musa A and B genomes separated. By combining sequence data with quantitative real-time PCR it was determined that the different Musa rbcS gene family members are also often multiply represented in each genome, with the highest copy numbers in the B genome. Expression of some of the rbcS genes varied in intensity and in different tissues indicating differences in regulation. To analyse and compare regulatory sequences of Musa rbcS genes, promoter and terminator regions were cloned for three Musa rbcS genes. Transient transformation assays using promoterreporterterminator constructs in maize, wheat, and sugarcane demonstrated that the rbcS-Ma1, rbcS-Ma3, and rbcS-Ma5 promoters could be useful for transgene expression in heterologous expression systems. Furthermore, the rbcS-Ma1 terminator resulted in a 2-fold increase of transgene expression when directly compared with the widely used Nos terminator.</abstract><subject><genre>keywords</genre><topic>Gene expression</topic><topic>intron</topic><topic>Musa</topic><topic>phylogenomic analysis</topic><topic>promoter</topic><topic>rbcS</topic><topic>RuBisCo</topic><topic>terminator</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Experimental Botany</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0022-0957</identifier><identifier type="eISSN">1460-2431</identifier><identifier type="PublisherID">exbotj</identifier><identifier type="PublisherID-hwp">jexbot</identifier><part><date>2007</date><detail type="volume"><caption>vol.</caption><number>58</number></detail><detail type="issue"><caption>no.</caption><number>10</number></detail><extent unit="pages"><start>2685</start><end>2697</end></extent></part></relatedItem><identifier type="istex">17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA</identifier><identifier type="DOI">10.1093/jxb/erm129</identifier><accessCondition type="use and reproduction" contentType="open-access">This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</accessCondition><recordInfo><recordContentSource>OUP</recordContentSource></recordInfo></mods></metadata><covers><json:item><original>true</original><mimetype>image/tiff</mimetype><extension>tiff</extension><uri>https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/covers/tiff</uri></json:item><json:item><original>true</original><mimetype>text/html</mimetype><extension>html</extension><uri>https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/covers/html</uri></json:item></covers><annexes><json:item><original>true</original><mimetype>image/jpeg</mimetype><extension>jpeg</extension><uri>https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/annexes/jpeg</uri></json:item><json:item><original>true</original><mimetype>image/gif</mimetype><extension>gif</extension><uri>https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/annexes/gif</uri></json:item></annexes><enrichments><istex:catWosTEI uri="https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/enrichments/catWos"><teiHeader><profileDesc><textClass><classCode scheme="WOS">PLANT SCIENCES</classCode></textClass></profileDesc></teiHeader></istex:catWosTEI><json:item><type>refBibs</type><uri>https://api.istex.fr/document/17729EB829CEBE3E8F744DCDB7A8EB20C7B280FA/enrichments/refBibs</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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