Biosynthesis of Taxadiene in Saccharomyces cerevisiae : selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy
Identification of efficient key enzymes in biosynthesis pathway and optimization of the fitness between functional modules and chassis are important for improving the production of target compounds. In this study, the taxadiene biosynthesis pathway was firstly constructed in yeast by transforming ts...
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| creator | Ding, Ming-Zhu Yan, Hui-Fang Li, Lin-Feng Zhai, Fang Shang, Lu-Qing Yin, Zheng Yuan, Ying-Jin |
| description | Identification of efficient key enzymes in biosynthesis pathway and optimization of the fitness between functional modules and chassis are important for improving the production of target compounds. In this study, the taxadiene biosynthesis pathway was firstly constructed in yeast by transforming ts gene and overexpressing erg20 and thmgr. Then, the catalytic capabilities of six different geranylgeranyl diphosphate synthases (GGPPS), the key enzyme in mevalonic acid (MVA) pathway catalyzing famesyl diphosphate (FPP) to geranylgeranyl diphosphate (GGPP), were predicted using enzyme-substrate docking strategy. GGPPSs from Taxus baccata x Taxus cuspidate (GGPPSbc), Erwinia herbicola (GGPPSeh), and S. cerevisiae (GGPPSsc) which ranked 1st, 4th and 6th in docking with FPP were selected for construction. The experimental results were consistent with the computer prediction that the engineered yeast with GGPPSbc exhibited the highest production. In addition, two chassis YSG50 and W303-1A were chosen, and the titer of taxadiene reached 72.8 mg/L in chassis YSG50 with GGPPSbc. Metabolomic study revealed that the contents of tricarboxylic acid cycle (TCA) intermediates and their precursor amino acids in chassis YSG50 was lower than those in W303-1A, indicating less carbon flux was divided into TCA cycle. Furthermore, the levels of TCA intermediates in the taxadiene producing yeasts were lower than those in chassis YSG50. Thus, it may result in more carbon flux in MVA pathway in chassis YSG50, which suggested that YSG50 was more suitable for engineering the taxadiene producing yeast. These results indicated that computer-aided protein modeling directed isoenzyme selection strategy and metabolomic study could guide the rational design of terpenes biosynthetic cells. |
| doi_str_mv | 10.1371/journal.pone.0109348 |
| format | Article |
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In this study, the taxadiene biosynthesis pathway was firstly constructed in yeast by transforming ts gene and overexpressing erg20 and thmgr. Then, the catalytic capabilities of six different geranylgeranyl diphosphate synthases (GGPPS), the key enzyme in mevalonic acid (MVA) pathway catalyzing famesyl diphosphate (FPP) to geranylgeranyl diphosphate (GGPP), were predicted using enzyme-substrate docking strategy. GGPPSs from Taxus baccata x Taxus cuspidate (GGPPSbc), Erwinia herbicola (GGPPSeh), and S. cerevisiae (GGPPSsc) which ranked 1st, 4th and 6th in docking with FPP were selected for construction. The experimental results were consistent with the computer prediction that the engineered yeast with GGPPSbc exhibited the highest production. In addition, two chassis YSG50 and W303-1A were chosen, and the titer of taxadiene reached 72.8 mg/L in chassis YSG50 with GGPPSbc. Metabolomic study revealed that the contents of tricarboxylic acid cycle (TCA) intermediates and their precursor amino acids in chassis YSG50 was lower than those in W303-1A, indicating less carbon flux was divided into TCA cycle. Furthermore, the levels of TCA intermediates in the taxadiene producing yeasts were lower than those in chassis YSG50. Thus, it may result in more carbon flux in MVA pathway in chassis YSG50, which suggested that YSG50 was more suitable for engineering the taxadiene producing yeast. These results indicated that computer-aided protein modeling directed isoenzyme selection strategy and metabolomic study could guide the rational design of terpenes biosynthetic cells.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0109348</identifier><identifier>PMID: 25295588</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Alkenes - metabolism ; Amino acids ; Baking yeast ; Bioengineering ; Biology and Life Sciences ; Biosynthesis ; Catalysis ; Chassis ; Chemical engineering ; Collaboration ; Computer and Information Sciences ; Diterpenes - metabolism ; Docking ; E coli ; Education ; Engineering and Technology ; Enzymes ; Escherichia coli ; Evolution & development ; Fitness ; Intermediates ; Laboratories ; Metabolism ; Metabolites ; Metabolomics ; Mevalonate pathway ; Mevalonic acid ; Natural products ; Optimization ; Pharmacy ; Polyisoprenyl Phosphates - metabolism ; Predictions ; Proteins ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae - metabolism ; Saccharomyces cerevisiae Proteins - metabolism ; Science ; Strategy ; Substrates ; Synthetic biology ; Terpenes ; Tricarboxylic acid cycle ; Ts gene ; Yeast ; Yeasts</subject><ispartof>PloS one, 2014-10, Vol.9 (10), p.e109348-e109348</ispartof><rights>2014 Ding 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>2014 Ding et al 2014 Ding et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c577t-8788954933f07564ccea23f8cc1356d8935aebd396c54d4f1d0cc93e945106f93</citedby><cites>FETCH-LOGICAL-c577t-8788954933f07564ccea23f8cc1356d8935aebd396c54d4f1d0cc93e945106f93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190181/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190181/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,866,887,2106,2932,23875,27933,27934,53800,53802</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25295588$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ling, Feng</contributor><creatorcontrib>Ding, Ming-Zhu</creatorcontrib><creatorcontrib>Yan, Hui-Fang</creatorcontrib><creatorcontrib>Li, Lin-Feng</creatorcontrib><creatorcontrib>Zhai, Fang</creatorcontrib><creatorcontrib>Shang, Lu-Qing</creatorcontrib><creatorcontrib>Yin, Zheng</creatorcontrib><creatorcontrib>Yuan, Ying-Jin</creatorcontrib><title>Biosynthesis of Taxadiene in Saccharomyces cerevisiae : selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Identification of efficient key enzymes in biosynthesis pathway and optimization of the fitness between functional modules and chassis are important for improving the production of target compounds. In this study, the taxadiene biosynthesis pathway was firstly constructed in yeast by transforming ts gene and overexpressing erg20 and thmgr. Then, the catalytic capabilities of six different geranylgeranyl diphosphate synthases (GGPPS), the key enzyme in mevalonic acid (MVA) pathway catalyzing famesyl diphosphate (FPP) to geranylgeranyl diphosphate (GGPP), were predicted using enzyme-substrate docking strategy. GGPPSs from Taxus baccata x Taxus cuspidate (GGPPSbc), Erwinia herbicola (GGPPSeh), and S. cerevisiae (GGPPSsc) which ranked 1st, 4th and 6th in docking with FPP were selected for construction. The experimental results were consistent with the computer prediction that the engineered yeast with GGPPSbc exhibited the highest production. In addition, two chassis YSG50 and W303-1A were chosen, and the titer of taxadiene reached 72.8 mg/L in chassis YSG50 with GGPPSbc. Metabolomic study revealed that the contents of tricarboxylic acid cycle (TCA) intermediates and their precursor amino acids in chassis YSG50 was lower than those in W303-1A, indicating less carbon flux was divided into TCA cycle. Furthermore, the levels of TCA intermediates in the taxadiene producing yeasts were lower than those in chassis YSG50. Thus, it may result in more carbon flux in MVA pathway in chassis YSG50, which suggested that YSG50 was more suitable for engineering the taxadiene producing yeast. These results indicated that computer-aided protein modeling directed isoenzyme selection strategy and metabolomic study could guide the rational design of terpenes biosynthetic cells.</description><subject>Alkenes - metabolism</subject><subject>Amino acids</subject><subject>Baking yeast</subject><subject>Bioengineering</subject><subject>Biology and Life Sciences</subject><subject>Biosynthesis</subject><subject>Catalysis</subject><subject>Chassis</subject><subject>Chemical engineering</subject><subject>Collaboration</subject><subject>Computer and Information Sciences</subject><subject>Diterpenes - metabolism</subject><subject>Docking</subject><subject>E coli</subject><subject>Education</subject><subject>Engineering and Technology</subject><subject>Enzymes</subject><subject>Escherichia coli</subject><subject>Evolution & development</subject><subject>Fitness</subject><subject>Intermediates</subject><subject>Laboratories</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Metabolomics</subject><subject>Mevalonate pathway</subject><subject>Mevalonic acid</subject><subject>Natural products</subject><subject>Optimization</subject><subject>Pharmacy</subject><subject>Polyisoprenyl Phosphates - metabolism</subject><subject>Predictions</subject><subject>Proteins</subject><subject>Saccharomyces cerevisiae</subject><subject>Saccharomyces cerevisiae - metabolism</subject><subject>Saccharomyces cerevisiae Proteins - metabolism</subject><subject>Science</subject><subject>Strategy</subject><subject>Substrates</subject><subject>Synthetic biology</subject><subject>Terpenes</subject><subject>Tricarboxylic acid cycle</subject><subject>Ts gene</subject><subject>Yeast</subject><subject>Yeasts</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</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>eNptks9u1DAQxiMEoqXwBggscellFzu2E4dDJaj4U6kSB8rZcsaTXS9ZO9jZirxInxdvN61axMnW-Pt-nhl9RfGa0SXjNXu_CbvoTb8cgsclZbThQj0pjlnDy0VVUv70wf2oeJHShlLJVVU9L45KWTZSKnVc3HxyIU1-XGNyiYSOXJk_xjr0SJwnPwzA2sSwnQATAYx47ZIzSD6QhD3C6ILfm1YYjZ_6-SDWDeuQhrUZkdzCTcJcjNmAlrQTMQTCdtiNGBfG2VyzAX45vyJpjNm0ml4WzzrTJ3w1nyfFzy-fr86_LS6_f704_3i5AFnX40LVSjVSNJx3tJaVAEBT8k4BMC4rqxouDbaWNxVIYUXHLAVoODZCMlp1DT8p3h64Qx-SnleaNKvyOplgNc2Ki4PCBrPRQ3RbEycdjNO3hRBX2sTRQY8aZEmVgS6jQVQZkZvrrGw7JXhb2jazzubfdu0WLaDP4_aPoI9fvFvrVbjWgjWUKZYBpzMght87TKPeugTY98Zj2O37Zvs9KKmy9N0_0v9PJw4qiCGliN19M4zqfczuXHofMz3HLNvePBzk3nSXK_4XP8fUQw</recordid><startdate>20141008</startdate><enddate>20141008</enddate><creator>Ding, Ming-Zhu</creator><creator>Yan, Hui-Fang</creator><creator>Li, Lin-Feng</creator><creator>Zhai, Fang</creator><creator>Shang, Lu-Qing</creator><creator>Yin, Zheng</creator><creator>Yuan, Ying-Jin</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>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></search><sort><creationdate>20141008</creationdate><title>Biosynthesis of Taxadiene in Saccharomyces cerevisiae : selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy</title><author>Ding, Ming-Zhu ; Yan, Hui-Fang ; Li, Lin-Feng ; Zhai, Fang ; Shang, Lu-Qing ; Yin, Zheng ; Yuan, Ying-Jin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c577t-8788954933f07564ccea23f8cc1356d8935aebd396c54d4f1d0cc93e945106f93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Alkenes - 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In this study, the taxadiene biosynthesis pathway was firstly constructed in yeast by transforming ts gene and overexpressing erg20 and thmgr. Then, the catalytic capabilities of six different geranylgeranyl diphosphate synthases (GGPPS), the key enzyme in mevalonic acid (MVA) pathway catalyzing famesyl diphosphate (FPP) to geranylgeranyl diphosphate (GGPP), were predicted using enzyme-substrate docking strategy. GGPPSs from Taxus baccata x Taxus cuspidate (GGPPSbc), Erwinia herbicola (GGPPSeh), and S. cerevisiae (GGPPSsc) which ranked 1st, 4th and 6th in docking with FPP were selected for construction. The experimental results were consistent with the computer prediction that the engineered yeast with GGPPSbc exhibited the highest production. In addition, two chassis YSG50 and W303-1A were chosen, and the titer of taxadiene reached 72.8 mg/L in chassis YSG50 with GGPPSbc. Metabolomic study revealed that the contents of tricarboxylic acid cycle (TCA) intermediates and their precursor amino acids in chassis YSG50 was lower than those in W303-1A, indicating less carbon flux was divided into TCA cycle. Furthermore, the levels of TCA intermediates in the taxadiene producing yeasts were lower than those in chassis YSG50. Thus, it may result in more carbon flux in MVA pathway in chassis YSG50, which suggested that YSG50 was more suitable for engineering the taxadiene producing yeast. These results indicated that computer-aided protein modeling directed isoenzyme selection strategy and metabolomic study could guide the rational design of terpenes biosynthetic cells.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25295588</pmid><doi>10.1371/journal.pone.0109348</doi><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Alkenes - metabolism Amino acids Baking yeast Bioengineering Biology and Life Sciences Biosynthesis Catalysis Chassis Chemical engineering Collaboration Computer and Information Sciences Diterpenes - metabolism Docking E coli Education Engineering and Technology Enzymes Escherichia coli Evolution & development Fitness Intermediates Laboratories Metabolism Metabolites Metabolomics Mevalonate pathway Mevalonic acid Natural products Optimization Pharmacy Polyisoprenyl Phosphates - metabolism Predictions Proteins Saccharomyces cerevisiae Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - metabolism Science Strategy Substrates Synthetic biology Terpenes Tricarboxylic acid cycle Ts gene Yeast Yeasts |
| title | Biosynthesis of Taxadiene in Saccharomyces cerevisiae : selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-01T01%3A36%3A40IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Biosynthesis%20of%20Taxadiene%20in%20Saccharomyces%20cerevisiae%20:%20selection%20of%20geranylgeranyl%20diphosphate%20synthase%20directed%20by%20a%20computer-aided%20docking%20strategy&rft.jtitle=PloS%20one&rft.au=Ding,%20Ming-Zhu&rft.date=2014-10-08&rft.volume=9&rft.issue=10&rft.spage=e109348&rft.epage=e109348&rft.pages=e109348-e109348&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0109348&rft_dat=%3Cproquest_plos_%3E3455733451%3C/proquest_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1609314170&rft_id=info:pmid/25295588&rft_doaj_id=oai_doaj_org_article_c5208acf106c46609889fd5bf843b2db&rfr_iscdi=true |