Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) Makino by comprehensive analysis of RNA and proteome sequencing
Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this stud...
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| creator | Zhang, Yangmei Chen, Qicong Huang, Yuanheng Zhao, Ruiqiang Sun, Jian Yuan, Xidong Xu, Huiming Liu, Huiyu Wu, Yaosheng |
| description | Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this study, a combination of isobaric tags for relative and absolute quantification (iTRAQ) proteome analysis and RNA sequencing transcriptome analysis was performed to identify the proteins and genes related to gypenoside biosynthesis. A total of 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. Seventeen cytochrome P450 (CYP) and 11 uridine 5'-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found. Seven putative CYPs (CYP71B19, CYP77A3, CYP86A7, CYP86A8, CYP89A2, CYP90A1, CYP94A1) and five putative UGTs (UGT73B4, UGT76B1, UGT74F2, UGT91C1 and UGT91A1) were selected as candidate structural modifiers of triterpenoid saponins, which were cloned for gene expression analysis. Comprehensive analysis of RNA sequencing and proteome sequencing showed that some CYPs and UGTs were found at both the transcription and translation levels. In this study, an expression analysis of 7 CYPs and 5 UGTs that contributed to gypenoside biosynthesis and distribution in G. pentaphyllum was performed, providing consistent results that will inspire more future research on vital genes/proteins involved in gypenoside biosynthesis. |
| doi_str_mv | 10.1371/journal.pone.0260027 |
| format | Article |
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Makino by comprehensive analysis of RNA and proteome sequencing</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Public Library of Science (PLoS)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Zhang, Yangmei ; Chen, Qicong ; Huang, Yuanheng ; Zhao, Ruiqiang ; Sun, Jian ; Yuan, Xidong ; Xu, Huiming ; Liu, Huiyu ; Wu, Yaosheng</creator><contributor>Chen, Shilin</contributor><creatorcontrib>Zhang, Yangmei ; Chen, Qicong ; Huang, Yuanheng ; Zhao, Ruiqiang ; Sun, Jian ; Yuan, Xidong ; Xu, Huiming ; Liu, Huiyu ; Wu, Yaosheng ; Chen, Shilin</creatorcontrib><description>Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this study, a combination of isobaric tags for relative and absolute quantification (iTRAQ) proteome analysis and RNA sequencing transcriptome analysis was performed to identify the proteins and genes related to gypenoside biosynthesis. A total of 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. Seventeen cytochrome P450 (CYP) and 11 uridine 5'-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found. Seven putative CYPs (CYP71B19, CYP77A3, CYP86A7, CYP86A8, CYP89A2, CYP90A1, CYP94A1) and five putative UGTs (UGT73B4, UGT76B1, UGT74F2, UGT91C1 and UGT91A1) were selected as candidate structural modifiers of triterpenoid saponins, which were cloned for gene expression analysis. Comprehensive analysis of RNA sequencing and proteome sequencing showed that some CYPs and UGTs were found at both the transcription and translation levels. In this study, an expression analysis of 7 CYPs and 5 UGTs that contributed to gypenoside biosynthesis and distribution in G. pentaphyllum was performed, providing consistent results that will inspire more future research on vital genes/proteins involved in gypenoside biosynthesis.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0260027</identifier><identifier>PMID: 34874937</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Antifungal agents ; Biochemistry ; Biology and Life Sciences ; Biosynthesis ; Chromatography, Liquid ; Cloning, Molecular ; Cucurbitaceae ; Cytochrome ; Cytochrome P-450 Enzyme System - genetics ; Cytochrome P-450 Enzyme System - metabolism ; Cytochrome P450 ; Cytochromes P450 ; Excavation ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene sequencing ; Genes ; Genetic aspects ; Glucuronosyltransferase ; Glucuronosyltransferase - genetics ; Glucuronosyltransferase - metabolism ; Gynostemma - genetics ; Gynostemma - growth & development ; Gynostemma - metabolism ; Higher education ; Laboratories ; Medicine ; Molecular biology ; Peptides ; Plant Extracts - biosynthesis ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Protein expression ; Proteins ; Proteomes ; Proteomics ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA sequencing ; Saponins ; Sequence Analysis, RNA ; Tandem Mass Spectrometry ; Transcription ; Transcriptomes ; UDP-glucuronosyltransferase ; Uridine</subject><ispartof>PloS one, 2021-12, Vol.16 (12), p.e0260027-e0260027</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Zhang et al 2021 Zhang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c593t-f2c778083b453cddb234abbc4c2b333d3153780f69a770e1813761f202543b5f3</citedby><cites>FETCH-LOGICAL-c593t-f2c778083b453cddb234abbc4c2b333d3153780f69a770e1813761f202543b5f3</cites><orcidid>0000-0002-3903-5361 ; 0000-0003-0501-8026</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8651138/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8651138/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2095,2914,23846,27903,27904,53769,53771,79346,79347</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34874937$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Chen, Shilin</contributor><creatorcontrib>Zhang, Yangmei</creatorcontrib><creatorcontrib>Chen, Qicong</creatorcontrib><creatorcontrib>Huang, Yuanheng</creatorcontrib><creatorcontrib>Zhao, Ruiqiang</creatorcontrib><creatorcontrib>Sun, Jian</creatorcontrib><creatorcontrib>Yuan, Xidong</creatorcontrib><creatorcontrib>Xu, Huiming</creatorcontrib><creatorcontrib>Liu, Huiyu</creatorcontrib><creatorcontrib>Wu, Yaosheng</creatorcontrib><title>Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) Makino by comprehensive analysis of RNA and proteome sequencing</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this study, a combination of isobaric tags for relative and absolute quantification (iTRAQ) proteome analysis and RNA sequencing transcriptome analysis was performed to identify the proteins and genes related to gypenoside biosynthesis. A total of 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. Seventeen cytochrome P450 (CYP) and 11 uridine 5'-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found. Seven putative CYPs (CYP71B19, CYP77A3, CYP86A7, CYP86A8, CYP89A2, CYP90A1, CYP94A1) and five putative UGTs (UGT73B4, UGT76B1, UGT74F2, UGT91C1 and UGT91A1) were selected as candidate structural modifiers of triterpenoid saponins, which were cloned for gene expression analysis. Comprehensive analysis of RNA sequencing and proteome sequencing showed that some CYPs and UGTs were found at both the transcription and translation levels. In this study, an expression analysis of 7 CYPs and 5 UGTs that contributed to gypenoside biosynthesis and distribution in G. pentaphyllum was performed, providing consistent results that will inspire more future research on vital genes/proteins involved in gypenoside biosynthesis.</description><subject>Analysis</subject><subject>Antifungal agents</subject><subject>Biochemistry</subject><subject>Biology and Life Sciences</subject><subject>Biosynthesis</subject><subject>Chromatography, Liquid</subject><subject>Cloning, Molecular</subject><subject>Cucurbitaceae</subject><subject>Cytochrome</subject><subject>Cytochrome P-450 Enzyme System - genetics</subject><subject>Cytochrome P-450 Enzyme System - metabolism</subject><subject>Cytochrome P450</subject><subject>Cytochromes P450</subject><subject>Excavation</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Glucuronosyltransferase</subject><subject>Glucuronosyltransferase - genetics</subject><subject>Glucuronosyltransferase - metabolism</subject><subject>Gynostemma - genetics</subject><subject>Gynostemma - growth & development</subject><subject>Gynostemma - metabolism</subject><subject>Higher education</subject><subject>Laboratories</subject><subject>Medicine</subject><subject>Molecular biology</subject><subject>Peptides</subject><subject>Plant Extracts - biosynthesis</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Protein expression</subject><subject>Proteins</subject><subject>Proteomes</subject><subject>Proteomics</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>Saponins</subject><subject>Sequence Analysis, RNA</subject><subject>Tandem Mass Spectrometry</subject><subject>Transcription</subject><subject>Transcriptomes</subject><subject>UDP-glucuronosyltransferase</subject><subject>Uridine</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptU02P0zAQjRCIXQr_AIElLsuhJbGdxL2sVFVQVlo-hLoHTpY_Jq1LYgc7WZGfyr_BbbOrLVrl4Njz3vOb8UySvM7SWUbK7MPO9d6KetY6C7MUF2mKyyfJeTYneFrglDx98H-WvAhhl6Y5YUXxPDkjlJV0Tsrz5O8KLCD4o8St6IyzSFgdt62HEI5bUQ_BBOQqtPz5_RC-Wa2Rh1p0oFHnULcF1LrQocZpUw3GblDoxAb2lM3QgnXBaEDSuDDYCN6rGYtWQwx00DQCRUwn2u1Q132DLtbb3srZe_RF_DLWITkg5ZpoaAs2mFs4sfTj6-JgqfWuA9cACvC7B6uiiZfJs0rUAV6N6yS5-fRxvfw8vf62ulourqcqn5NuWmFVlixlRNKcKK0lJlRIqajCkhCiSZaTGK-KuSjLFDIWi19kFU5xTonMKzJJ3h5129oFPr5K4PFBynwehcuIuDoitBM73nrTCD9wJww_HDi_4cJ3RtXASQ6EYUyZoEAJ01IpVkiNy5yxXGIctS7H23rZgFaxcl7UJ6KnEWu2fONuOSvyLCMsClyMAt7FUoWONyYoqGthwfUH3zHFjMZemSTv_oM-nt2I2oiYgLGVi_eqvShfFCwvKaaURNTsEVT8NDRGxRauTDw_IdAjQXkXgofqPscs5fsBuDPD9wPAxwGItDcP63NPuut48g86ggZ-</recordid><startdate>20211207</startdate><enddate>20211207</enddate><creator>Zhang, Yangmei</creator><creator>Chen, Qicong</creator><creator>Huang, Yuanheng</creator><creator>Zhao, Ruiqiang</creator><creator>Sun, Jian</creator><creator>Yuan, Xidong</creator><creator>Xu, Huiming</creator><creator>Liu, Huiyu</creator><creator>Wu, Yaosheng</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-3903-5361</orcidid><orcidid>https://orcid.org/0000-0003-0501-8026</orcidid></search><sort><creationdate>20211207</creationdate><title>Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Yangmei</au><au>Chen, Qicong</au><au>Huang, Yuanheng</au><au>Zhao, Ruiqiang</au><au>Sun, Jian</au><au>Yuan, Xidong</au><au>Xu, Huiming</au><au>Liu, Huiyu</au><au>Wu, Yaosheng</au><au>Chen, Shilin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) Makino by comprehensive analysis of RNA and proteome sequencing</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-12-07</date><risdate>2021</risdate><volume>16</volume><issue>12</issue><spage>e0260027</spage><epage>e0260027</epage><pages>e0260027-e0260027</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this study, a combination of isobaric tags for relative and absolute quantification (iTRAQ) proteome analysis and RNA sequencing transcriptome analysis was performed to identify the proteins and genes related to gypenoside biosynthesis. A total of 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. Seventeen cytochrome P450 (CYP) and 11 uridine 5'-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found. Seven putative CYPs (CYP71B19, CYP77A3, CYP86A7, CYP86A8, CYP89A2, CYP90A1, CYP94A1) and five putative UGTs (UGT73B4, UGT76B1, UGT74F2, UGT91C1 and UGT91A1) were selected as candidate structural modifiers of triterpenoid saponins, which were cloned for gene expression analysis. Comprehensive analysis of RNA sequencing and proteome sequencing showed that some CYPs and UGTs were found at both the transcription and translation levels. In this study, an expression analysis of 7 CYPs and 5 UGTs that contributed to gypenoside biosynthesis and distribution in G. pentaphyllum was performed, providing consistent results that will inspire more future research on vital genes/proteins involved in gypenoside biosynthesis.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34874937</pmid><doi>10.1371/journal.pone.0260027</doi><orcidid>https://orcid.org/0000-0002-3903-5361</orcidid><orcidid>https://orcid.org/0000-0003-0501-8026</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2021-12, Vol.16 (12), p.e0260027-e0260027 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2607598087 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Antifungal agents Biochemistry Biology and Life Sciences Biosynthesis Chromatography, Liquid Cloning, Molecular Cucurbitaceae Cytochrome Cytochrome P-450 Enzyme System - genetics Cytochrome P-450 Enzyme System - metabolism Cytochrome P450 Cytochromes P450 Excavation Gene expression Gene Expression Profiling Gene Expression Regulation, Neoplastic Gene sequencing Genes Genetic aspects Glucuronosyltransferase Glucuronosyltransferase - genetics Glucuronosyltransferase - metabolism Gynostemma - genetics Gynostemma - growth & development Gynostemma - metabolism Higher education Laboratories Medicine Molecular biology Peptides Plant Extracts - biosynthesis Plant Proteins - genetics Plant Proteins - metabolism Protein expression Proteins Proteomes Proteomics Research and Analysis Methods Ribonucleic acid RNA RNA sequencing Saponins Sequence Analysis, RNA Tandem Mass Spectrometry Transcription Transcriptomes UDP-glucuronosyltransferase Uridine |
| title | Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) Makino by comprehensive analysis of RNA and proteome sequencing |
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