Stress Responsive Proteins Are Actively Regulated during Rice (Oryza sativa) Embryogenesis as Indicated by Quantitative Proteomics Analysis
Identifieur interne : 000980 ( Pmc/Checkpoint ); précédent : 000979; suivant : 000981Stress Responsive Proteins Are Actively Regulated during Rice (Oryza sativa) Embryogenesis as Indicated by Quantitative Proteomics Analysis
Auteurs : Jin Zi [République populaire de Chine] ; Jiyuan Zhang [République populaire de Chine] ; Quanhui Wang [République populaire de Chine] ; Baojin Zhou [République populaire de Chine] ; Junyan Zhong [République populaire de Chine] ; Chaoliang Zhang [République populaire de Chine] ; Xuemei Qiu [République populaire de Chine] ; Bo Wen [République populaire de Chine] ; Shenyan Zhang [République populaire de Chine] ; Xiqin Fu [République populaire de Chine] ; Liang Lin [République populaire de Chine] ; Siqi Liu [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.
Url:
DOI: 10.1371/journal.pone.0074229
PubMed: 24058531
PubMed Central: 3776822
Affiliations:
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de Chine</country><wicri:regionArea>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Jiyuan" sort="Zhang, Jiyuan" uniqKey="Zhang J" first="Jiyuan" last="Zhang">Jiyuan Zhang</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>College of Biological Sciences, China Agricultural University, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Quanhui" sort="Wang, Quanhui" uniqKey="Wang Q" first="Quanhui" last="Wang">Quanhui Wang</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhou, Baojin" sort="Zhou, Baojin" uniqKey="Zhou B" first="Baojin" last="Zhou">Baojin Zhou</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhong, Junyan" sort="Zhong, Junyan" uniqKey="Zhong J" first="Junyan" last="Zhong">Junyan Zhong</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhang, Chaoliang" sort="Zhang, Chaoliang" uniqKey="Zhang C" first="Chaoliang" last="Zhang">Chaoliang Zhang</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Qiu, Xuemei" sort="Qiu, Xuemei" uniqKey="Qiu X" first="Xuemei" last="Qiu">Xuemei Qiu</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Wen, Bo" sort="Wen, Bo" uniqKey="Wen B" first="Bo" last="Wen">Bo Wen</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhang, Shenyan" sort="Zhang, Shenyan" uniqKey="Zhang S" first="Shenyan" last="Zhang">Shenyan Zhang</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Fu, Xiqin" sort="Fu, Xiqin" uniqKey="Fu X" first="Xiqin" last="Fu">Xiqin Fu</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Hunan Hybrid Rice Research Center, Changsha, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hunan Hybrid Rice Research Center, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Liang" sort="Lin, Liang" uniqKey="Lin L" first="Liang" last="Lin">Liang Lin</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Liu, Siqi" sort="Liu, Siqi" uniqKey="Liu S" first="Siqi" last="Liu">Siqi Liu</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Proteomics Division, BGI-Shenzhen, Shenzhen</wicri:regionArea><placeName><settlement type="city">Shenzhen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="De Smet, I" uniqKey="De Smet I">I De Smet</name></author><author><name sortKey="Lau, S" uniqKey="Lau S">S Lau</name></author><author><name sortKey="Mayer, U" uniqKey="Mayer U">U Mayer</name></author><author><name sortKey="Jurgens, G" uniqKey="Jurgens G">G Jurgens</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Itoh, J" uniqKey="Itoh J">J Itoh</name></author><author><name sortKey="Nonomura, K" uniqKey="Nonomura K">K Nonomura</name></author><author><name sortKey="Ikeda, K" uniqKey="Ikeda K">K Ikeda</name></author><author><name sortKey="Yamaki, S" uniqKey="Yamaki S">S Yamaki</name></author><author><name sortKey="Inukai, Y" uniqKey="Inukai Y">Y Inukai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dam, S" 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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">24058531</article-id><article-id pub-id-type="pmc">3776822</article-id><article-id pub-id-type="publisher-id">PONE-D-13-20827</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0074229</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Stress Responsive Proteins Are Actively Regulated during Rice (<italic>Oryza sativa</italic>) Embryogenesis as Indicated by Quantitative Proteomics Analysis</article-title><alt-title alt-title-type="running-head">Quantitative Proteomics of Rice Embryogenesis</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zi</surname><given-names>Jin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Jiyuan</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Quanhui</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Baojin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhong</surname><given-names>Junyan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Chaoliang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Qiu</surname><given-names>Xuemei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wen</surname><given-names>Bo</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Shenyan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fu</surname><given-names>Xiqin</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Liang</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>Liu</surname><given-names>Siqi</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Proteomics Division, BGI-Shenzhen, Shenzhen, China</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China</addr-line></aff><aff id="aff3"><label>3</label><addr-line>College of Biological Sciences, China Agricultural University, Beijing, China</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Hunan Hybrid Rice Research Center, Changsha, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>De Smet</surname><given-names>Ive</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Nottingham, United Kingdom</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>linl@genomics.cn</email> (LL); <email>siqiliu@genomics.cn</email> (SL)</corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: SL LL QW J. Zi. Performed the experiments: J. Zi J. Zhang CZ XQ BZ. Analyzed the data: J. Zi J. Zhong BW SZ. Contributed reagents/materials/analysis tools: XF. Wrote the paper: J. Zi LL SL.</p></fn></author-notes><pub-date pub-type="collection"><year>2013</year></pub-date><pub-date pub-type="epub"><day>18</day><month>9</month><year>2013</year></pub-date><volume>8</volume><issue>9</issue><elocation-id>e74229</elocation-id><history><date date-type="received"><day>21</day><month>5</month><year>2013</year></date><date date-type="accepted"><day>28</day><month>7</month><year>2013</year></date></history><permissions><copyright-year>2013</copyright-year><copyright-holder>Zi et al</copyright-holder><license><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 credited.</license-p></license></permissions><abstract><p>Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.</p></abstract><funding-group><funding-statement>This work was supported by the National High Technology 863 Research and Development Program of China 2012AA020204,the National Key Basic Research 973 Program of China 2010CB912703, the Natural Science Foundation of China 91131009 and the Guangdong Innovative Research Team Program 2009010016. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="10"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Guangdong</li></region><settlement><li>Pékin</li><li>Shenzhen</li></settlement></list><tree><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Zi, Jin" sort="Zi, Jin" uniqKey="Zi J" first="Jin" last="Zi">Jin Zi</name></region><name sortKey="Fu, Xiqin" sort="Fu, Xiqin" uniqKey="Fu X" first="Xiqin" last="Fu">Xiqin Fu</name><name sortKey="Lin, Liang" sort="Lin, Liang" uniqKey="Lin L" first="Liang" last="Lin">Liang Lin</name><name sortKey="Liu, Siqi" sort="Liu, Siqi" uniqKey="Liu S" first="Siqi" last="Liu">Siqi Liu</name><name sortKey="Liu, Siqi" sort="Liu, Siqi" uniqKey="Liu S" first="Siqi" last="Liu">Siqi Liu</name><name sortKey="Qiu, Xuemei" sort="Qiu, Xuemei" uniqKey="Qiu X" first="Xuemei" last="Qiu">Xuemei Qiu</name><name sortKey="Wang, Quanhui" sort="Wang, Quanhui" uniqKey="Wang Q" first="Quanhui" last="Wang">Quanhui Wang</name><name sortKey="Wang, Quanhui" sort="Wang, Quanhui" uniqKey="Wang Q" first="Quanhui" last="Wang">Quanhui Wang</name><name sortKey="Wen, Bo" sort="Wen, Bo" uniqKey="Wen B" first="Bo" last="Wen">Bo Wen</name><name sortKey="Zhang, Chaoliang" sort="Zhang, Chaoliang" uniqKey="Zhang C" first="Chaoliang" last="Zhang">Chaoliang Zhang</name><name sortKey="Zhang, Jiyuan" sort="Zhang, Jiyuan" uniqKey="Zhang J" first="Jiyuan" last="Zhang">Jiyuan Zhang</name><name sortKey="Zhang, Jiyuan" sort="Zhang, Jiyuan" uniqKey="Zhang J" first="Jiyuan" last="Zhang">Jiyuan Zhang</name><name sortKey="Zhang, Shenyan" sort="Zhang, Shenyan" uniqKey="Zhang S" first="Shenyan" last="Zhang">Shenyan Zhang</name><name sortKey="Zhang, Shenyan" sort="Zhang, Shenyan" uniqKey="Zhang S" first="Shenyan" last="Zhang">Shenyan Zhang</name><name sortKey="Zhong, Junyan" sort="Zhong, Junyan" uniqKey="Zhong J" first="Junyan" last="Zhong">Junyan Zhong</name><name sortKey="Zhou, Baojin" sort="Zhou, Baojin" uniqKey="Zhou B" first="Baojin" last="Zhou">Baojin Zhou</name><name sortKey="Zi, Jin" sort="Zi, Jin" uniqKey="Zi J" first="Jin" last="Zi">Jin Zi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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