Acclimation of bacterial cell state for high-throughput enzyme engineering using a DmpR-dependent transcriptional activation system
Genetic circuit-based biosensors have emerged as an effective analytical tool in synthetic biology; these biosensors can be applied to high-throughput screening of new biocatalysts and metabolic pathways. Sigma 54 (σ 54 )-dependent transcription factor (TF) can be a valuable component of these biose...
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description | Genetic circuit-based biosensors have emerged as an effective analytical tool in synthetic biology; these biosensors can be applied to high-throughput screening of new biocatalysts and metabolic pathways. Sigma 54 (σ
54
)-dependent transcription factor (TF) can be a valuable component of these biosensors owing to its intrinsic silent property compared to most of the housekeeping sigma 70 (σ
70
) TFs. Here, we show that these unique characteristics of σ
54
-dependent TFs can be used to control the host cell state to be more appropriate for high-throughput screening. The acclimation of cell state was achieved by using guanosine (penta)tetraphosphate ((p)ppGpp)-related genes (
relA
,
spoT
) and nutrient conditions, to link the σ
54
TF-based reporter expression with the target enzyme activity. By controlling stringent programmed responses and optimizing assay conditions, catalytically improved tyrosine phenol lyase (TPL) enzymes were successfully obtained using a σ
54
-dependent DmpR as the TF component, demonstrating the practical feasibility of this biosensor. This combinatorial strategy of biosensors using σ factor-dependent TFs will allow for more effective high-throughput enzyme engineering with broad applicability. |
doi_str_mv | 10.1038/s41598-020-62892-1 |
format | Article |
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54
)-dependent transcription factor (TF) can be a valuable component of these biosensors owing to its intrinsic silent property compared to most of the housekeeping sigma 70 (σ
70
) TFs. Here, we show that these unique characteristics of σ
54
-dependent TFs can be used to control the host cell state to be more appropriate for high-throughput screening. The acclimation of cell state was achieved by using guanosine (penta)tetraphosphate ((p)ppGpp)-related genes (
relA
,
spoT
) and nutrient conditions, to link the σ
54
TF-based reporter expression with the target enzyme activity. By controlling stringent programmed responses and optimizing assay conditions, catalytically improved tyrosine phenol lyase (TPL) enzymes were successfully obtained using a σ
54
-dependent DmpR as the TF component, demonstrating the practical feasibility of this biosensor. This combinatorial strategy of biosensors using σ factor-dependent TFs will allow for more effective high-throughput enzyme engineering with broad applicability.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-020-62892-1</identifier><identifier>PMID: 32269250</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/1647/2163 ; 631/553/2697 ; 631/553/552 ; Acclimation ; Acclimatization ; Bacterial Proteins - genetics ; Biocatalysts ; Biosensing Techniques - methods ; Biosensors ; Enzymatic activity ; Enzymes ; Escherichia coli ; Escherichia coli Proteins - genetics ; Escherichia coli Proteins - metabolism ; GTP Pyrophosphokinase - genetics ; GTP Pyrophosphokinase - metabolism ; Guanosine ; High-throughput screening ; High-Throughput Screening Assays - methods ; Humanities and Social Sciences ; Metabolic pathways ; multidisciplinary ; Phenols ; Promoter Regions, Genetic ; Protein Engineering - methods ; Pseudomonas putida ; Pyrophosphatases - genetics ; Pyrophosphatases - metabolism ; RelA protein ; Science ; Science (multidisciplinary) ; Sigma Factor - genetics ; Sigma Factor - metabolism ; Trans-Activators - genetics ; Transcription activation ; Transcriptional Activation ; Tyrosine Phenol-Lyase - genetics ; Tyrosine Phenol-Lyase - metabolism</subject><ispartof>Scientific reports, 2020-04, Vol.10 (1), p.6091-6091, Article 6091</ispartof><rights>The Author(s) 2020</rights><rights>The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c511t-268460c1ff6c0bf2fda007a2593c0fc4df1d59dbcc5005a2d6de49b3c5481dda3</citedby><cites>FETCH-LOGICAL-c511t-268460c1ff6c0bf2fda007a2593c0fc4df1d59dbcc5005a2d6de49b3c5481dda3</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/PMC7142073/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142073/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32269250$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kwon, Kil Koang</creatorcontrib><creatorcontrib>Yeom, Soo-Jin</creatorcontrib><creatorcontrib>Choi, Su-Lim</creatorcontrib><creatorcontrib>Rha, Eugene</creatorcontrib><creatorcontrib>Lee, Hyewon</creatorcontrib><creatorcontrib>Kim, Haseong</creatorcontrib><creatorcontrib>Lee, Dae-Hee</creatorcontrib><creatorcontrib>Lee, Seung-Goo</creatorcontrib><title>Acclimation of bacterial cell state for high-throughput enzyme engineering using a DmpR-dependent transcriptional activation system</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Genetic circuit-based biosensors have emerged as an effective analytical tool in synthetic biology; these biosensors can be applied to high-throughput screening of new biocatalysts and metabolic pathways. Sigma 54 (σ
54
)-dependent transcription factor (TF) can be a valuable component of these biosensors owing to its intrinsic silent property compared to most of the housekeeping sigma 70 (σ
70
) TFs. Here, we show that these unique characteristics of σ
54
-dependent TFs can be used to control the host cell state to be more appropriate for high-throughput screening. The acclimation of cell state was achieved by using guanosine (penta)tetraphosphate ((p)ppGpp)-related genes (
relA
,
spoT
) and nutrient conditions, to link the σ
54
TF-based reporter expression with the target enzyme activity. By controlling stringent programmed responses and optimizing assay conditions, catalytically improved tyrosine phenol lyase (TPL) enzymes were successfully obtained using a σ
54
-dependent DmpR as the TF component, demonstrating the practical feasibility of this biosensor. This combinatorial strategy of biosensors using σ factor-dependent TFs will allow for more effective high-throughput enzyme engineering with broad applicability.</description><subject>631/1647/2163</subject><subject>631/553/2697</subject><subject>631/553/552</subject><subject>Acclimation</subject><subject>Acclimatization</subject><subject>Bacterial Proteins - genetics</subject><subject>Biocatalysts</subject><subject>Biosensing Techniques - methods</subject><subject>Biosensors</subject><subject>Enzymatic activity</subject><subject>Enzymes</subject><subject>Escherichia coli</subject><subject>Escherichia coli Proteins - genetics</subject><subject>Escherichia coli Proteins - metabolism</subject><subject>GTP Pyrophosphokinase - genetics</subject><subject>GTP Pyrophosphokinase - metabolism</subject><subject>Guanosine</subject><subject>High-throughput screening</subject><subject>High-Throughput Screening Assays - methods</subject><subject>Humanities and Social Sciences</subject><subject>Metabolic pathways</subject><subject>multidisciplinary</subject><subject>Phenols</subject><subject>Promoter Regions, Genetic</subject><subject>Protein Engineering - methods</subject><subject>Pseudomonas putida</subject><subject>Pyrophosphatases - genetics</subject><subject>Pyrophosphatases - metabolism</subject><subject>RelA protein</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Sigma Factor - genetics</subject><subject>Sigma Factor - metabolism</subject><subject>Trans-Activators - genetics</subject><subject>Transcription activation</subject><subject>Transcriptional Activation</subject><subject>Tyrosine Phenol-Lyase - genetics</subject><subject>Tyrosine Phenol-Lyase - metabolism</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9Uctu1TAUtBAVrUp_gAWyxIZNwM_cZINUtbQgVUKqytpy_EhcJXawnUqXLT-O07SlsMALH8ueM3PGA8AbjD5gRJuPiWHeNhUiqKpJ05IKvwBHBDFeEUrIy2fnQ3CS0i0qi5OW4fYVOCy3dUs4OgK_TpUa3SSzCx4GCzupsolOjlCZcYQpy2ygDREOrh-qPMSw9MO8ZGj8z_1kSumdN6XD93BJ6y7h-TRfV9rMxmvjM8xR-qSim1eNQlwU3N0mmPYpm-k1OLByTObkoR6D7xefb86-VFffLr-enV5VimOcK1I3rEYKW1sr1FlitURoJwlvqUJWMW2x5q3ulOLFqiS61oa1HVWcNVhrSY_Bp413XrrJaFWGi3IUcyz-414E6cTfL94Nog93YocZQTtaCN4_EMTwYzEpi8ml9Z-kN2FJgtCmQYjhmhXou3-gt2GJxf49alfTEkZTUGRDqRhSisY-DYORWGMWW8yixCzuYxa4NL19buOp5THUAqAbIM1rLib-0f4P7W9NoLcq</recordid><startdate>20200408</startdate><enddate>20200408</enddate><creator>Kwon, Kil Koang</creator><creator>Yeom, Soo-Jin</creator><creator>Choi, Su-Lim</creator><creator>Rha, Eugene</creator><creator>Lee, Hyewon</creator><creator>Kim, Haseong</creator><creator>Lee, Dae-Hee</creator><creator>Lee, Seung-Goo</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><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>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200408</creationdate><title>Acclimation of bacterial cell state for high-throughput enzyme engineering using a DmpR-dependent transcriptional activation system</title><author>Kwon, Kil Koang ; Yeom, Soo-Jin ; Choi, Su-Lim ; Rha, Eugene ; Lee, Hyewon ; Kim, Haseong ; Lee, Dae-Hee ; Lee, Seung-Goo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c511t-268460c1ff6c0bf2fda007a2593c0fc4df1d59dbcc5005a2d6de49b3c5481dda3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>631/1647/2163</topic><topic>631/553/2697</topic><topic>631/553/552</topic><topic>Acclimation</topic><topic>Acclimatization</topic><topic>Bacterial Proteins - genetics</topic><topic>Biocatalysts</topic><topic>Biosensing Techniques - methods</topic><topic>Biosensors</topic><topic>Enzymatic activity</topic><topic>Enzymes</topic><topic>Escherichia coli</topic><topic>Escherichia coli Proteins - genetics</topic><topic>Escherichia coli Proteins - metabolism</topic><topic>GTP Pyrophosphokinase - genetics</topic><topic>GTP Pyrophosphokinase - metabolism</topic><topic>Guanosine</topic><topic>High-throughput screening</topic><topic>High-Throughput Screening Assays - methods</topic><topic>Humanities and Social Sciences</topic><topic>Metabolic pathways</topic><topic>multidisciplinary</topic><topic>Phenols</topic><topic>Promoter Regions, Genetic</topic><topic>Protein Engineering - methods</topic><topic>Pseudomonas putida</topic><topic>Pyrophosphatases - genetics</topic><topic>Pyrophosphatases - metabolism</topic><topic>RelA protein</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Sigma Factor - genetics</topic><topic>Sigma Factor - metabolism</topic><topic>Trans-Activators - genetics</topic><topic>Transcription activation</topic><topic>Transcriptional Activation</topic><topic>Tyrosine Phenol-Lyase - genetics</topic><topic>Tyrosine Phenol-Lyase - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kwon, Kil Koang</creatorcontrib><creatorcontrib>Yeom, Soo-Jin</creatorcontrib><creatorcontrib>Choi, Su-Lim</creatorcontrib><creatorcontrib>Rha, Eugene</creatorcontrib><creatorcontrib>Lee, Hyewon</creatorcontrib><creatorcontrib>Kim, Haseong</creatorcontrib><creatorcontrib>Lee, Dae-Hee</creatorcontrib><creatorcontrib>Lee, Seung-Goo</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kwon, Kil Koang</au><au>Yeom, Soo-Jin</au><au>Choi, Su-Lim</au><au>Rha, Eugene</au><au>Lee, Hyewon</au><au>Kim, Haseong</au><au>Lee, Dae-Hee</au><au>Lee, Seung-Goo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Acclimation of bacterial cell state for high-throughput enzyme engineering using a DmpR-dependent transcriptional activation system</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2020-04-08</date><risdate>2020</risdate><volume>10</volume><issue>1</issue><spage>6091</spage><epage>6091</epage><pages>6091-6091</pages><artnum>6091</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Genetic circuit-based biosensors have emerged as an effective analytical tool in synthetic biology; these biosensors can be applied to high-throughput screening of new biocatalysts and metabolic pathways. Sigma 54 (σ
54
)-dependent transcription factor (TF) can be a valuable component of these biosensors owing to its intrinsic silent property compared to most of the housekeeping sigma 70 (σ
70
) TFs. Here, we show that these unique characteristics of σ
54
-dependent TFs can be used to control the host cell state to be more appropriate for high-throughput screening. The acclimation of cell state was achieved by using guanosine (penta)tetraphosphate ((p)ppGpp)-related genes (
relA
,
spoT
) and nutrient conditions, to link the σ
54
TF-based reporter expression with the target enzyme activity. By controlling stringent programmed responses and optimizing assay conditions, catalytically improved tyrosine phenol lyase (TPL) enzymes were successfully obtained using a σ
54
-dependent DmpR as the TF component, demonstrating the practical feasibility of this biosensor. This combinatorial strategy of biosensors using σ factor-dependent TFs will allow for more effective high-throughput enzyme engineering with broad applicability.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>32269250</pmid><doi>10.1038/s41598-020-62892-1</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; Nature Free; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry; Springer Nature OA Free Journals |
subjects | 631/1647/2163 631/553/2697 631/553/552 Acclimation Acclimatization Bacterial Proteins - genetics Biocatalysts Biosensing Techniques - methods Biosensors Enzymatic activity Enzymes Escherichia coli Escherichia coli Proteins - genetics Escherichia coli Proteins - metabolism GTP Pyrophosphokinase - genetics GTP Pyrophosphokinase - metabolism Guanosine High-throughput screening High-Throughput Screening Assays - methods Humanities and Social Sciences Metabolic pathways multidisciplinary Phenols Promoter Regions, Genetic Protein Engineering - methods Pseudomonas putida Pyrophosphatases - genetics Pyrophosphatases - metabolism RelA protein Science Science (multidisciplinary) Sigma Factor - genetics Sigma Factor - metabolism Trans-Activators - genetics Transcription activation Transcriptional Activation Tyrosine Phenol-Lyase - genetics Tyrosine Phenol-Lyase - metabolism |
title | Acclimation of bacterial cell state for high-throughput enzyme engineering using a DmpR-dependent transcriptional activation system |
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