An integrative analysis of transcriptome and proteome provides new insights into carotenoid biosynthesis and regulation in sweet orange fruits.
Identifieur interne : 000F56 ( Ncbi/Checkpoint ); précédent : 000F55; suivant : 000F57An integrative analysis of transcriptome and proteome provides new insights into carotenoid biosynthesis and regulation in sweet orange fruits.
Auteurs : Zhiyong Pan [République populaire de Chine] ; Yunliu Zeng ; Jianyong An ; Junli Ye ; Qiang Xu ; Xiuxin DengSource :
- Journal of proteomics [ 1876-7737 ] ; 2012.
English descriptors
- KwdEn :
- Carotenoids (biosynthesis), Citrus sinensis (genetics), Citrus sinensis (metabolism), Gene Expression Regulation, Plant, Genes, Plant (physiology), Heat-Shock Proteins (genetics), Oxidative Stress (genetics), Proteome (metabolism), Proteomics, RNA, Messenger (metabolism), Transcription Factors (genetics), Transcriptome (physiology).
- MESH :
- chemical , biosynthesis : Carotenoids.
- genetics : Citrus sinensis, Heat-Shock Proteins, Oxidative Stress, Transcription Factors.
- metabolism : Citrus sinensis, Proteome, RNA, Messenger.
- physiology : Genes, Plant, Transcriptome.
- Gene Expression Regulation, Plant, Proteomics.
Abstract
An integrative analysis of transcriptome and proteome was performed to identify differential genes/proteins of a red-flesh sweet orange Cara Cara in comparison with a common cultivar Newhall at ripening stages. At the transcript level, gene expression was measured with Massively Parallel Signature Sequencing (MPSS), and 629 genes of these two sweet orange cultivars differed by two fold or more (FDR<0.001). At the protein level, a combination of 2DE and MALDI-TOF-TOF MS identified 48 protein spots differed in relative abundance (P<0.05). The data obtained from comparing transcriptome with proteome showed a poor correlation, suggesting the necessity to integrate both transcriptomic and proteomic approaches in order to get a comprehensive molecular characterization. Function analysis of the differential genes/proteins revealed that a set of candidates was associated with carotenoid biosynthesis and the regulation. Overall, some intriguing genes/proteins were previously unrecognized related with the formation of red-flesh trait, which provided new insights into molecular processes regulating lycopene accumulation in a red-flesh sweet orange. In addition, some genes/proteins were found to be different in expression patterns between the Cara Cara and another red-flesh sweet orange Hong Anliu, and their potential roles were further discussed in the present study.
DOI: 10.1016/j.jprot.2012.03.016
PubMed: 22472342
Affiliations:
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last="Zeng">Yunliu Zeng</name></author><author><name sortKey="An, Jianyong" sort="An, Jianyong" uniqKey="An J" first="Jianyong" last="An">Jianyong An</name></author><author><name sortKey="Ye, Junli" sort="Ye, Junli" uniqKey="Ye J" first="Junli" last="Ye">Junli Ye</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22472342</idno><idno type="pmid">22472342</idno><idno type="doi">10.1016/j.jprot.2012.03.016</idno><idno type="wicri:Area/PubMed/Corpus">000607</idno><idno type="wicri:Area/PubMed/Curation">000607</idno><idno type="wicri:Area/PubMed/Checkpoint">000607</idno><idno type="wicri:Area/Ncbi/Merge">000F56</idno><idno 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430070</wicri:noRegion></affiliation></author><author><name sortKey="Zeng, Yunliu" sort="Zeng, Yunliu" uniqKey="Zeng Y" first="Yunliu" last="Zeng">Yunliu Zeng</name></author><author><name sortKey="An, Jianyong" sort="An, Jianyong" uniqKey="An J" first="Jianyong" last="An">Jianyong An</name></author><author><name sortKey="Ye, Junli" sort="Ye, Junli" uniqKey="Ye J" first="Junli" last="Ye">Junli Ye</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name></author></analytic><series><title level="j">Journal of proteomics</title><idno type="eISSN">1876-7737</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Carotenoids (biosynthesis)</term><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (metabolism)</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant (physiology)</term><term>Heat-Shock Proteins (genetics)</term><term>Oxidative Stress (genetics)</term><term>Proteome (metabolism)</term><term>Proteomics</term><term>RNA, Messenger (metabolism)</term><term>Transcription Factors (genetics)</term><term>Transcriptome (physiology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Carotenoids</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Heat-Shock Proteins</term><term>Oxidative Stress</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Citrus sinensis</term><term>Proteome</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Genes, Plant</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Proteomics</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An integrative analysis of transcriptome and proteome was performed to identify differential genes/proteins of a red-flesh sweet orange Cara Cara in comparison with a common cultivar Newhall at ripening stages. At the transcript level, gene expression was measured with Massively Parallel Signature Sequencing (MPSS), and 629 genes of these two sweet orange cultivars differed by two fold or more (FDR<0.001). At the protein level, a combination of 2DE and MALDI-TOF-TOF MS identified 48 protein spots differed in relative abundance (P<0.05). The data obtained from comparing transcriptome with proteome showed a poor correlation, suggesting the necessity to integrate both transcriptomic and proteomic approaches in order to get a comprehensive molecular characterization. Function analysis of the differential genes/proteins revealed that a set of candidates was associated with carotenoid biosynthesis and the regulation. Overall, some intriguing genes/proteins were previously unrecognized related with the formation of red-flesh trait, which provided new insights into molecular processes regulating lycopene accumulation in a red-flesh sweet orange. In addition, some genes/proteins were found to be different in expression patterns between the Cara Cara and another red-flesh sweet orange Hong Anliu, and their potential roles were further discussed in the present study.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="An, Jianyong" sort="An, Jianyong" uniqKey="An J" first="Jianyong" last="An">Jianyong An</name><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><name sortKey="Ye, Junli" sort="Ye, Junli" uniqKey="Ye J" first="Junli" last="Ye">Junli Ye</name><name sortKey="Zeng, Yunliu" sort="Zeng, Yunliu" uniqKey="Zeng Y" first="Yunliu" last="Zeng">Yunliu Zeng</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Pan, Zhiyong" sort="Pan, Zhiyong" uniqKey="Pan Z" first="Zhiyong" last="Pan">Zhiyong Pan</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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