Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification
Identifieur interne : 000087 ( Main/Exploration ); précédent : 000086; suivant : 000088Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification
Auteurs : Lulu Xie [République populaire de Chine] ; Pingli Liu [République populaire de Chine] ; Zhixin Zhu [République populaire de Chine] ; Shifan Zhang [République populaire de Chine] ; Shujiang Zhang [République populaire de Chine] ; Fei Li [République populaire de Chine] ; Hui Zhang [République populaire de Chine] ; Guoliang Li [République populaire de Chine] ; Yunxiao Wei [République populaire de Chine] ; Rifei Sun [République populaire de Chine]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2016.
Abstract
Polyketide synthases (PKSs) utilize the products of primary metabolism to synthesize a wide array of secondary metabolites in both prokaryotic and eukaryotic organisms. PKSs can be grouped into three distinct classes, types I, II, and III, based on enzyme structure, substrate specificity, and catalytic mechanisms. The type III PKS enzymes function as homodimers, and are the only class of PKS that do not require acyl carrier protein. Plant type III PKS enzymes, also known as chalcone synthase (CHS)-like enzymes, are of particular interest due to their functional diversity. In this study, we mined type III
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DOI: 10.3389/fpls.2016.01312
PubMed: 27625671
PubMed Central: 5004622
Affiliations:
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Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Shujiang" sort="Zhang, Shujiang" uniqKey="Zhang S" first="Shujiang" last="Zhang">Shujiang Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Li, Fei" sort="Li, Fei" uniqKey="Li F" first="Fei" last="Li">Fei Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Hui" sort="Zhang, Hui" uniqKey="Zhang H" first="Hui" last="Zhang">Hui Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Li, Guoliang" sort="Li, Guoliang" uniqKey="Li G" first="Guoliang" last="Li">Guoliang Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Wei, Yunxiao" sort="Wei, Yunxiao" uniqKey="Wei Y" first="Yunxiao" last="Wei">Yunxiao Wei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Sun, Rifei" sort="Sun, Rifei" uniqKey="Sun R" first="Rifei" last="Sun">Rifei Sun</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27625671</idno><idno type="pmc">5004622</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004622</idno><idno type="RBID">PMC:5004622</idno><idno type="doi">10.3389/fpls.2016.01312</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000F38</idno><idno type="wicri:Area/Pmc/Curation">000F37</idno><idno type="wicri:Area/Pmc/Checkpoint">000069</idno><idno type="wicri:Area/Ncbi/Merge">002173</idno><idno type="wicri:Area/Ncbi/Curation">002173</idno><idno type="wicri:Area/Ncbi/Checkpoint">002173</idno><idno type="wicri:Area/Main/Merge">000087</idno><idno type="wicri:Area/Main/Curation">000087</idno><idno type="wicri:Area/Main/Exploration">000087</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification</title><author><name sortKey="Xie, Lulu" sort="Xie, Lulu" uniqKey="Xie L" first="Lulu" last="Xie">Lulu Xie</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Liu, Pingli" sort="Liu, Pingli" uniqKey="Liu P" first="Pingli" last="Liu">Pingli Liu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>College of Biological Sciences and Biotechnology, Beijing Forestry University</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Zhixin" sort="Zhu, Zhixin" uniqKey="Zhu Z" first="Zhixin" last="Zhu">Zhixin Zhu</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>College of Horticulture and Landscape Architecture, Hainan University</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Shifan" sort="Zhang, Shifan" uniqKey="Zhang S" first="Shifan" last="Zhang">Shifan Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Shujiang" sort="Zhang, Shujiang" uniqKey="Zhang S" first="Shujiang" last="Zhang">Shujiang Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Li, Fei" sort="Li, Fei" uniqKey="Li F" first="Fei" last="Li">Fei Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Hui" sort="Zhang, Hui" uniqKey="Zhang H" first="Hui" last="Zhang">Hui Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Li, Guoliang" sort="Li, Guoliang" uniqKey="Li G" first="Guoliang" last="Li">Guoliang Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Wei, Yunxiao" sort="Wei, Yunxiao" uniqKey="Wei Y" first="Yunxiao" last="Wei">Yunxiao Wei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Sun, Rifei" sort="Sun, Rifei" uniqKey="Sun R" first="Rifei" last="Sun">Rifei Sun</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution><country>Beijing, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Polyketide synthases (PKSs) utilize the products of primary metabolism to synthesize a wide array of secondary metabolites in both prokaryotic and eukaryotic organisms. PKSs can be grouped into three distinct classes, types I, II, and III, based on enzyme structure, substrate specificity, and catalytic mechanisms. The type III PKS enzymes function as homodimers, and are the only class of PKS that do not require acyl carrier protein. Plant type III PKS enzymes, also known as chalcone synthase (CHS)-like enzymes, are of particular interest due to their functional diversity. In this study, we mined type III <italic>PKS</italic> gene sequences from the genomes of six aquatic algae and 25 land plants (1 bryophyte, 1 lycophyte, 2 basal angiosperms, 16 core eudicots, and 5 monocots). <italic>PKS III</italic> sequences were found relatively conserved in all embryophytes, but not exist in algae. We also examined gene expression patterns by analyzing available transcriptome data, and identified potential <italic>cis</italic>-regulatory elements in upstream sequences. Phylogenetic trees of dicots angiosperms showed that plant type III PKS proteins fall into three clades. Clade A contains CHS/STS-type enzymes coding genes with diverse transcriptional expression patterns and enzymatic functions, while clade B is further divided into subclades b1 and b2, which consist of anther-specific CHS-like enzymes. Differentiation regions, such as amino acids 196-207 between clades A and B, and predicted positive selected sites within α-helixes in late appeared branches of clade A, account for the major diversification in substrate choice and catalytic reaction. The integrity and location of conserved <italic>cis</italic>-elements containing MYB and bHLH binding sites can affect transcription levels. Potential binding sites for transcription factors such as WRKY, SPL, or AP2/EREBP may contribute to tissue- or taxon-specific differences in gene expression. Our data shows that gene duplications and functional diversification of plant type III PKS enzymes played a critical role in the ancient conquest of the land by early plants and angiosperm diversification.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abe, T" uniqKey="Abe T">T. Abe</name></author><author><name sortKey="Morita, H" uniqKey="Morita H">H. Morita</name></author><author><name sortKey="Noma, H" uniqKey="Noma H">H. Noma</name></author><author><name sortKey="Kohno, T" uniqKey="Kohno T">T. Kohno</name></author><author><name sortKey="Noguchi, H" uniqKey="Noguchi H">H. Noguchi</name></author><author><name sortKey="Abe, I" uniqKey="Abe I">I. Abe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Adams, K L" uniqKey="Adams K">K. L. Adams</name></author><author><name sortKey="Wendel, J F" uniqKey="Wendel J">J. F. 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Tang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Xie, Lulu" sort="Xie, Lulu" uniqKey="Xie L" first="Lulu" last="Xie">Lulu Xie</name></noRegion><name sortKey="Li, Fei" sort="Li, Fei" uniqKey="Li F" first="Fei" last="Li">Fei Li</name><name sortKey="Li, Guoliang" sort="Li, Guoliang" uniqKey="Li G" first="Guoliang" last="Li">Guoliang Li</name><name sortKey="Liu, Pingli" sort="Liu, Pingli" uniqKey="Liu P" first="Pingli" last="Liu">Pingli Liu</name><name sortKey="Sun, Rifei" sort="Sun, Rifei" uniqKey="Sun R" first="Rifei" last="Sun">Rifei Sun</name><name sortKey="Wei, Yunxiao" sort="Wei, Yunxiao" uniqKey="Wei Y" first="Yunxiao" last="Wei">Yunxiao Wei</name><name sortKey="Zhang, Hui" sort="Zhang, Hui" uniqKey="Zhang H" first="Hui" last="Zhang">Hui Zhang</name><name sortKey="Zhang, Shifan" sort="Zhang, Shifan" uniqKey="Zhang S" first="Shifan" last="Zhang">Shifan Zhang</name><name sortKey="Zhang, Shujiang" sort="Zhang, Shujiang" uniqKey="Zhang S" first="Shujiang" last="Zhang">Shujiang Zhang</name><name sortKey="Zhu, Zhixin" sort="Zhu, Zhixin" uniqKey="Zhu Z" first="Zhixin" last="Zhu">Zhixin Zhu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification
}}
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| NlmPubMed2Wicri -a OrangerV1
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