142 lines
18 KiB
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142 lines
18 KiB
XML
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<mods:title id="6B6A42F461F71FC3178EC54A95D78CEF">De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway</mods:title>
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<mods:namePart id="37E0670B66C79BCCEB44167B14420182">Deshmukh, Aaditi B.</mods:namePart>
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<mods:affiliation id="A61E80DBCF0277F45491A1526BCE9A04">∗ & Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India</mods:affiliation>
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<mods:namePart id="733C2AD03037203B05BB657DBBFA49B6">Datir, Sagar S.</mods:namePart>
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<mods:namePart id="63AFBF2923D26CA8BB63B41A91B802A7">Bhonde, Yogesh</mods:namePart>
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<mods:namePart id="E35BEE17A14CB45AAE3ECFC1F3A86AE9">Kelkar, Natasha</mods:namePart>
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<mods:namePart id="E81BBB8F5959C3ADBD2DF5D75CC75DDC">Samdani, Pawan</mods:namePart>
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<mods:namePart id="D72A6969F25E382AFF4A88C80691D53F">Tamhane, Vaijayanti A.</mods:namePart>
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<mods:title id="678E1A8409ECBD7F22F0834E4816C342">Phytochemistry</mods:title>
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<treatment id="03881B7683587F01FCCDE8C78148FB28" LSID="urn:lsid:plazi:treatment:03881B7683587F01FCCDE8C78148FB28" httpUri="http://treatment.plazi.org/id/03881B7683587F01FCCDE8C78148FB28" lastPageId="5" lastPageNumber="205" pageId="4" pageNumber="205">
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<subSubSection id="C33BF9EB83587F00FCCDE8C785C5FB67" box="[818,1454,1206,1225]" pageId="4" pageNumber="205" type="nomenclature">
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<paragraph id="8B9EAA6083587F00FCCDE8C785C5FB67" blockId="4.[818,1454,1206,1225]" box="[818,1454,1206,1225]" pageId="4" pageNumber="205">
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<heading id="D0D61D0C83587F00FCCDE8C785C5FB67" bold="true" box="[818,1454,1206,1225]" fontSize="36" level="1" pageId="4" pageNumber="205" reason="1">
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<emphasis id="B955767283587F00FCCDE8C785C5FB67" bold="true" box="[818,1454,1206,1225]" italics="true" pageId="4" pageNumber="205">
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2.6. Transcription factor analysis in the
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<taxonomicName id="4C21D1E383587F00FB5FE8C78568FB67" authority="(L.) Kurz" box="[1184,1283,1206,1225]" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="4" pageNumber="205" phylum="Tracheophyta" rank="subSpecies" species="indicum" subSpecies="root">O. indicum</taxonomicName>
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root transcriptome
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</emphasis>
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</paragraph>
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<subSubSection id="C33BF9EB83587F01FCACE89F8148FB28" lastPageId="5" lastPageNumber="206" pageId="4" pageNumber="205" type="description">
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<paragraph id="8B9EAA6083587F00FCACE89F8440F90D" blockId="4.[818,1488,1262,1978]" pageId="4" pageNumber="205">
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At least six distinct transcription factors (TFs) namely myeloblastosis (MYB), basic helix-loop-helix (bHLH), WD or beta-transducin repeat (WD40), WRKY, Zinc finger and MADS box proteins are involved in flavonoid biosynthesis regulation (Terrier et al., 2009). Of these, three transcription factors MYB, bHLH and WD40 (MBW) were detected in the root transcriptome of
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<taxonomicName id="4C21D1E383587F00FB9EE90884A0FA22" box="[1121,1227,1401,1420]" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="4" pageNumber="205" phylum="Tracheophyta" rank="species" species="indicum">
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<emphasis id="B955767283587F00FB9EE90884A0FA22" bold="true" box="[1121,1227,1401,1420]" italics="true" pageId="4" pageNumber="205">O. indicum</emphasis>
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</taxonomicName>
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(
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<tableCitation id="C6A39FDB83587F00FB1FE9088545FA22" box="[1248,1326,1401,1420]" captionStart="Table 6" captionStartId="5.[121,171,161,178]" captionTargetPageId="5" captionText="Table 6 Transcription factors involved in flavonoid biosynthesis regulation in O. indicum root." pageId="4" pageNumber="205">Table 6</tableCitation>
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; Supplementary
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<tableCitation id="C6A39FDB83587F00FCCDE9E48312FA06" box="[818,889,1429,1448]" captionStart="Table 3" captionStartId="2.[101,151,1616,1633]" captionTargetBox="[117,753,1681,1969]" captionTargetPageId="2" captionText="Table 3 Number of O. indicum transcripts mapped to plants (top ten)." pageId="4" pageNumber="205">Table 3</tableCitation>
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). MYB11, MYB12 and MYB111 are known to control flavonol biosynthesis by activating the early biosynthetic steps (
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<bibRefCitation id="EFB0D79183587F00FACCE9C085A2FA6A" author="Nesi, N. & Debeaujon, I. & Jond, C. & Stewart, A. J. & Jenkins, G. I. & Caboche, M. & Lepiniec, L." box="[1331,1481,1457,1476]" pageId="4" pageNumber="205" pagination="2463 - 2479" refId="ref12827" refString="Nesi, N., Debeaujon, I., Jond, C., Stewart, A. J., Jenkins, G. I., Caboche, M., Lepiniec, L., 2002. The TRANSPARENT TESTA 16 locus encodes the Arabidopsis bsistermads domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell 14, 2463 - 2479." type="journal article" year="2002">Nesi et al., 2002</bibRefCitation>
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;
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<bibRefCitation id="EFB0D79183587F00FCCDE9BC83BAFA4E" author="Gou, J. Y. & Felippes, F. F. & Liu, C. J. & Weigel, D. & Wang, J. W." box="[818,977,1485,1504]" pageId="4" pageNumber="205" pagination="1512 - 1522" refId="ref11451" refString="Gou, J. Y., Felippes, F. F., Liu, C. J., Weigel, D., Wang, J. W., 2011. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR 156 - targeted SPL transcription factor. Plant Cell 23, 1512 - 1522." type="journal article" year="2011">Gou et al., 2011</bibRefCitation>
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), while the MBW complex activates the late biosynthetic genes of flavonoid biosynthesis (
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<bibRefCitation id="EFB0D79183587F00FB53E9988517FA52" author="Mehrtens, F. & Kranz, H. & Bednarek, P. & Weisshaar, B." box="[1196,1404,1513,1532]" pageId="4" pageNumber="205" pagination="1083 - 1096" refId="ref12682" refString="Mehrtens, F., Kranz, H., Bednarek, P., Weisshaar, B., 2005. The Arabidopsis transcription factor MYB 12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol. 138, 1083 - 1096." type="journal article" year="2005">Mehrtens et al., 2005</bibRefCitation>
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; Stracke et al., 2007;
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<bibRefCitation id="EFB0D79183587F00FC4FEA74846BF9B6" author="Li, S." box="[944,1024,1541,1560]" pageId="4" pageNumber="205" pagination="27522" refId="ref12361" refString="Li, S., 2014. Transcriptional control of flavonoid biosynthesis. Fine-tuning of the MYBbHLH-WD 40 (MBW) complex. Plant Signal. Behav. 9, e 27522." type="journal article" year="2014">Li, 2014</bibRefCitation>
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). In the
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<taxonomicName id="4C21D1E383587F00FBA6EA7484D6F9B6" box="[1113,1213,1541,1560]" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="4" pageNumber="206" phylum="Tracheophyta" rank="subSpecies" species="indicum" subSpecies="root">
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<emphasis id="B955767283587F00FBA6EA7484D6F9B6" bold="true" box="[1113,1213,1541,1560]" italics="true" pageId="4" pageNumber="205">O. indicum</emphasis>
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</taxonomicName>
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root, the MYB transcription factor family was represented prominently, followed by WD40 and bHLH (
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<tableCitation id="C6A39FDB83587F00FC8AEA4C83D0F9FE" box="[885,955,1597,1616]" captionStart="Table 6" captionStartId="5.[121,171,161,178]" captionTargetPageId="5" captionText="Table 6 Transcription factors involved in flavonoid biosynthesis regulation in O. indicum root." pageId="4" pageNumber="205">Table 6</tableCitation>
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; Supplementary
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<tableCitation id="C6A39FDB83587F00FBA6EA4C84F5F9FE" box="[1113,1182,1597,1616]" captionStart="Table 3" captionStartId="2.[101,151,1616,1633]" captionTargetBox="[117,753,1681,1969]" captionTargetPageId="2" captionText="Table 3 Number of O. indicum transcripts mapped to plants (top ten)." pageId="4" pageNumber="205">Table 3</tableCitation>
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). These transcription factors can either work individually or synergistically in controlling the multiple enzymatic steps involved in the flavonoid biosynthesis (
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<bibRefCitation id="EFB0D79183587F00FAA7EA048309F90D" author="Mano, H. & Ogasawara, F. & Sato, K. & Higo, H. & Minobe, Y." pageId="4" pageNumber="205" pagination="1252 - 1268" refId="ref12574" refString="Mano, H., Ogasawara, F., Sato, K., Higo, H., Minobe, Y., 2007. Isolation of a regulatory gene of anthocyanin biosynthesis in tuberous roots of purple-fleshed sweet potato. Plant Physiol. 143, 1252 - 1268." type="journal article" year="2007">Mano et al., 2007</bibRefCitation>
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;
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<bibRefCitation id="EFB0D79183587F00FC90EAE18475F90D" author="Hichri, I. & Barrieu, F. & Bogs, J. & Kappel, C. & Delrot, S. & Lauvergeat, V." box="[879,1054,1680,1699]" pageId="4" pageNumber="205" pagination="2465 - 2483" refId="ref11778" refString="Hichri, I., Barrieu, F., Bogs, J., Kappel, C., Delrot, S., Lauvergeat, V., 2011. Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J. Exp. Bot. 62, 2465 - 2483." type="journal article" year="2011">Hichri et al., 2011</bibRefCitation>
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).
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</paragraph>
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<paragraph id="8B9EAA6083587F01FCACEADD8148FB28" blockId="4.[818,1488,1262,1978]" lastBlockId="5.[100,770,1055,1158]" lastPageId="5" lastPageNumber="206" pageId="4" pageNumber="205">
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Among the MYB family TFs, MYB 4 and R2R3-MYB were highly abundant in
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<taxonomicName id="4C21D1E383587F00FC54EAB98465F975" box="[939,1038,1736,1755]" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="4" pageNumber="206" phylum="Tracheophyta" rank="subSpecies" species="indicum" subSpecies="root">
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<emphasis id="B955767283587F00FC54EAB98465F975" bold="true" box="[939,1038,1736,1755]" italics="true" pageId="4" pageNumber="205">O. indicum</emphasis>
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</taxonomicName>
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root (
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<tableCitation id="C6A39FDB83587F00FBB5EAB984F9F975" box="[1098,1170,1736,1755]" captionStart="Table 6" captionStartId="5.[121,171,161,178]" captionTargetPageId="5" captionText="Table 6 Transcription factors involved in flavonoid biosynthesis regulation in O. indicum root." pageId="4" pageNumber="205">Table 6</tableCitation>
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). R2R3-MYB protein is known to participate in the regulation of specialized metabolism including production of phenylpropanoids and flavonoids in plants (Vom Endt et al., 2002;
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<bibRefCitation id="EFB0D79183587F00FC92EB6D847DF881" author="Bomal, C. & Bedon, F. & Caron, S. & Mansfield, S. D. & Levasseur, C. & Cooke, J. E. & Blais, S. & Tremblay, L. & Morency, M. J. & Pavy, N. & Grima-Pettenati, J. & Seguin, A. & Mackay, J." box="[877,1046,1820,1839]" pageId="4" pageNumber="205" pagination="3925 - 3939" refId="ref10627" refString="Bomal, C., Bedon, F., Caron, S., Mansfield, S. D., Levasseur, C., Cooke, J. E., Blais, S., Tremblay, L., Morency, M. J., Pavy, N., Grima-Pettenati, J., Seguin, A., Mackay, J., 2008. Involvement of Pinus taeda MYB 1 and MYB 8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. J. Exp. Bot. 59, 3925 - 3939." type="journal article" year="2008">Bomal et al., 2008</bibRefCitation>
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; Taylor and Grotewold, 2005). The putative TF bHLH was highly expressed in the root transcriptome of
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<emphasis id="B955767283587F00FA9BEB4985BBF8E5" bold="true" box="[1380,1488,1848,1867]" italics="true" pageId="4" pageNumber="205">
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<taxonomicName id="4C21D1E383587F00FA9BEB4985A7F8E5" box="[1380,1484,1848,1867]" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="4" pageNumber="205" phylum="Tracheophyta" rank="species" species="indicum">O. indicum</taxonomicName>
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.
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</emphasis>
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bHLH interacts with R3 repeat domains of MYB proteins at the Nterminal acidic region to
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<taxonomicName id="4C21D1E383587F00FBD1EB0184D2F82D" authority="MYB" authorityName="MYB" box="[1070,1209,1904,1923]" form="the" pageId="4" pageNumber="205" rank="form">form the MYB</taxonomicName>
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–bHLH complex, involved in flavonoid biosynthesis pathway regulation (
|
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<bibRefCitation id="EFB0D79183587F00FB2BEBFA8514F830" author="Feller, A. & Machemer, K. & Braun, E. L. & Grotewold, E." box="[1236,1407,1931,1950]" pageId="4" pageNumber="205" pagination="94 - 116" refId="ref11246" refString="Feller, A., Machemer, K., Braun, E. L., Grotewold, E., 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 66, 94 - 116." type="journal article" year="2011">Feller et al., 2011</bibRefCitation>
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). Transducin/WD-40 family isoform 5, of the WD40 family was abundant in
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<taxonomicName id="4C21D1E383587F01FA45EBD680C0FB9C" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" lastPageId="5" lastPageNumber="206" order="Lamiales" pageId="4" pageNumber="205" phylum="Tracheophyta" rank="species" species="indicum">
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<emphasis id="B955767283587F01FA45EBD680C0FB9C" bold="true" italics="true" lastPageId="5" lastPageNumber="206" pageId="4" pageNumber="205">O. indicum</emphasis>
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</taxonomicName>
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roots. WD40 proteins do not possess any catalytic activity, but it has been hypothesized that they act as a docking platform for regulating the anthocyanin and phenylalanine biosynthesis pathways (
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<bibRefCitation id="EFB0D79183597F01FF93E802817EFB28" author="Feller, A. & Machemer, K. & Braun, E. L. & Grotewold, E." box="[108,277,1139,1158]" pageId="5" pageNumber="206" pagination="94 - 116" refId="ref11246" refString="Feller, A., Machemer, K., Braun, E. L., Grotewold, E., 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 66, 94 - 116." type="journal article" year="2011">Feller et al., 2011</bibRefCitation>
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).
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</paragraph>
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</subSubSection>
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</treatment>
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