Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage
Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at p...
Gespeichert in:
| Veröffentlicht in: | PloS one 2014-02, Vol.9 (2), p.e89580-e89580 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e89580 |
|---|---|
| container_issue | 2 |
| container_start_page | e89580 |
| container_title | PloS one |
| container_volume | 9 |
| creator | Royce, Liam A Boggess, Erin Fu, Yao Liu, Ping Shanks, Jacqueline V Dickerson, Julie Jarboe, Laura R |
| description | Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic. |
| doi_str_mv | 10.1371/journal.pone.0089580 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1503271627</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A478787742</galeid><doaj_id>oai_doaj_org_article_7d7c720b0634472e9e80fbcd4f29b44a</doaj_id><sourcerecordid>A478787742</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-4d7d63c89a0359415a37f29b571e42eccfb618107ede802f4fa7c6b705bc86af3</originalsourceid><addsrcrecordid>eNqNk99r1TAUx4sobk7_A9GCIPpwr2mSNqkPwhhTLwwGOn2NaXrSZqTNNWll97833e3GrexB8pBw8jnf8yM5SfIyQ-uMsOzDtRt9L-1663pYI8TLnKNHyXFWErwqMCKPD85HybMQrhHKCS-Kp8kRpjkvOOfHya8rL_ugvNkOrjMqlVFyF0xInU6V9JW72dnJrEydqlZaC30DqenT86Ba8Ea1RqbKWfMxrWDn-jrtoKuiJqS17GQDz5MnWtoAL-b9JPnx-fzq7Ovq4vLL5uz0YqWKEg8rWrO6IIqXEpG8pFkuCdO4rHKWAcWglK6KjGeIQQ0cYU21ZKqoGMorxQupyUnyeq-7tS6IuTlBZDkimGUFZpHY7InayWux9aaTfiecNOLW4HwjpB-MsiBYzRTDqEIFoZRhKGNMXamaTilRKqPWpznaWHVQK-gHL-1CdHnTm1Y07o8gJeGU0yjwbhbw7vcIYRCdCQqsjZ1z423edMqaTeibf9CHq5upRsYCTK9djKsmUXFKGY-LURyp9QNUXDXE148_SZtoXzi8XzhEZoCboZFjCGLz_dv_s5c_l-zbA7YFaYc2ODsOxvVhCdI9qLwLwYO-b3KGxDQId90Q0yCIeRCi26vDB7p3uvv55C9CAwO2</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1503271627</pqid></control><display><type>article</type><title>Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS) Journals Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Royce, Liam A ; Boggess, Erin ; Fu, Yao ; Liu, Ping ; Shanks, Jacqueline V ; Dickerson, Julie ; Jarboe, Laura R</creator><contributor>Misra, Rajeev</contributor><creatorcontrib>Royce, Liam A ; Boggess, Erin ; Fu, Yao ; Liu, Ping ; Shanks, Jacqueline V ; Dickerson, Julie ; Jarboe, Laura R ; Misra, Rajeev</creatorcontrib><description>Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0089580</identifier><identifier>PMID: 24586888</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Accumulation ; Acid resistance ; Acidification ; Amino acids ; Analysis ; Bioengineering ; Biology ; Biosynthesis ; Carboxylic acids ; Carboxylic Acids - metabolism ; Cell Membrane - metabolism ; Chemicals ; Computer engineering ; Cyclopropane ; Damage detection ; DNA binding proteins ; E coli ; Engineering ; Escherichia coli ; Escherichia coli - metabolism ; Escherichia coli Proteins - metabolism ; Ethanol ; Fatty acids ; Gene expression ; Gene Expression Regulation, Bacterial ; Genomes ; Glutamate ; Homeostasis ; Inorganic acids ; Intracellular ; Lipids ; Metabolism ; Microbiology ; Octanoic acid ; pH effects ; Plasmids ; Protonmotive force ; Saturated fatty acids ; Supplementation ; Supplements ; Toxicity ; Transcription factors</subject><ispartof>PloS one, 2014-02, Vol.9 (2), p.e89580-e89580</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Royce 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 Royce et al 2014 Royce et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-4d7d63c89a0359415a37f29b571e42eccfb618107ede802f4fa7c6b705bc86af3</citedby><cites>FETCH-LOGICAL-c692t-4d7d63c89a0359415a37f29b571e42eccfb618107ede802f4fa7c6b705bc86af3</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/PMC3938484/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938484/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2097,2916,23848,27906,27907,53773,53775,79350,79351</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24586888$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Misra, Rajeev</contributor><creatorcontrib>Royce, Liam A</creatorcontrib><creatorcontrib>Boggess, Erin</creatorcontrib><creatorcontrib>Fu, Yao</creatorcontrib><creatorcontrib>Liu, Ping</creatorcontrib><creatorcontrib>Shanks, Jacqueline V</creatorcontrib><creatorcontrib>Dickerson, Julie</creatorcontrib><creatorcontrib>Jarboe, Laura R</creatorcontrib><title>Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic.</description><subject>Accumulation</subject><subject>Acid resistance</subject><subject>Acidification</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Bioengineering</subject><subject>Biology</subject><subject>Biosynthesis</subject><subject>Carboxylic acids</subject><subject>Carboxylic Acids - metabolism</subject><subject>Cell Membrane - metabolism</subject><subject>Chemicals</subject><subject>Computer engineering</subject><subject>Cyclopropane</subject><subject>Damage detection</subject><subject>DNA binding proteins</subject><subject>E coli</subject><subject>Engineering</subject><subject>Escherichia coli</subject><subject>Escherichia coli - metabolism</subject><subject>Escherichia coli Proteins - metabolism</subject><subject>Ethanol</subject><subject>Fatty acids</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Genomes</subject><subject>Glutamate</subject><subject>Homeostasis</subject><subject>Inorganic acids</subject><subject>Intracellular</subject><subject>Lipids</subject><subject>Metabolism</subject><subject>Microbiology</subject><subject>Octanoic acid</subject><subject>pH effects</subject><subject>Plasmids</subject><subject>Protonmotive force</subject><subject>Saturated fatty acids</subject><subject>Supplementation</subject><subject>Supplements</subject><subject>Toxicity</subject><subject>Transcription factors</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>eNqNk99r1TAUx4sobk7_A9GCIPpwr2mSNqkPwhhTLwwGOn2NaXrSZqTNNWll97833e3GrexB8pBw8jnf8yM5SfIyQ-uMsOzDtRt9L-1663pYI8TLnKNHyXFWErwqMCKPD85HybMQrhHKCS-Kp8kRpjkvOOfHya8rL_ugvNkOrjMqlVFyF0xInU6V9JW72dnJrEydqlZaC30DqenT86Ba8Ea1RqbKWfMxrWDn-jrtoKuiJqS17GQDz5MnWtoAL-b9JPnx-fzq7Ovq4vLL5uz0YqWKEg8rWrO6IIqXEpG8pFkuCdO4rHKWAcWglK6KjGeIQQ0cYU21ZKqoGMorxQupyUnyeq-7tS6IuTlBZDkimGUFZpHY7InayWux9aaTfiecNOLW4HwjpB-MsiBYzRTDqEIFoZRhKGNMXamaTilRKqPWpznaWHVQK-gHL-1CdHnTm1Y07o8gJeGU0yjwbhbw7vcIYRCdCQqsjZ1z423edMqaTeibf9CHq5upRsYCTK9djKsmUXFKGY-LURyp9QNUXDXE148_SZtoXzi8XzhEZoCboZFjCGLz_dv_s5c_l-zbA7YFaYc2ODsOxvVhCdI9qLwLwYO-b3KGxDQId90Q0yCIeRCi26vDB7p3uvv55C9CAwO2</recordid><startdate>20140228</startdate><enddate>20140228</enddate><creator>Royce, Liam A</creator><creator>Boggess, Erin</creator><creator>Fu, Yao</creator><creator>Liu, Ping</creator><creator>Shanks, Jacqueline V</creator><creator>Dickerson, Julie</creator><creator>Jarboe, Laura R</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>IOV</scope><scope>ISR</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></search><sort><creationdate>20140228</creationdate><title>Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage</title><author>Royce, Liam A ; Boggess, Erin ; Fu, Yao ; Liu, Ping ; Shanks, Jacqueline V ; Dickerson, Julie ; Jarboe, Laura R</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-4d7d63c89a0359415a37f29b571e42eccfb618107ede802f4fa7c6b705bc86af3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Accumulation</topic><topic>Acid resistance</topic><topic>Acidification</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Bioengineering</topic><topic>Biology</topic><topic>Biosynthesis</topic><topic>Carboxylic acids</topic><topic>Carboxylic Acids - metabolism</topic><topic>Cell Membrane - metabolism</topic><topic>Chemicals</topic><topic>Computer engineering</topic><topic>Cyclopropane</topic><topic>Damage detection</topic><topic>DNA binding proteins</topic><topic>E coli</topic><topic>Engineering</topic><topic>Escherichia coli</topic><topic>Escherichia coli - metabolism</topic><topic>Escherichia coli Proteins - metabolism</topic><topic>Ethanol</topic><topic>Fatty acids</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Genomes</topic><topic>Glutamate</topic><topic>Homeostasis</topic><topic>Inorganic acids</topic><topic>Intracellular</topic><topic>Lipids</topic><topic>Metabolism</topic><topic>Microbiology</topic><topic>Octanoic acid</topic><topic>pH effects</topic><topic>Plasmids</topic><topic>Protonmotive force</topic><topic>Saturated fatty acids</topic><topic>Supplementation</topic><topic>Supplements</topic><topic>Toxicity</topic><topic>Transcription factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Royce, Liam A</creatorcontrib><creatorcontrib>Boggess, Erin</creatorcontrib><creatorcontrib>Fu, Yao</creatorcontrib><creatorcontrib>Liu, Ping</creatorcontrib><creatorcontrib>Shanks, Jacqueline V</creatorcontrib><creatorcontrib>Dickerson, Julie</creatorcontrib><creatorcontrib>Jarboe, Laura R</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology 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>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</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 China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - 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>Royce, Liam A</au><au>Boggess, Erin</au><au>Fu, Yao</au><au>Liu, Ping</au><au>Shanks, Jacqueline V</au><au>Dickerson, Julie</au><au>Jarboe, Laura R</au><au>Misra, Rajeev</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-02-28</date><risdate>2014</risdate><volume>9</volume><issue>2</issue><spage>e89580</spage><epage>e89580</epage><pages>e89580-e89580</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24586888</pmid><doi>10.1371/journal.pone.0089580</doi><tpages>e89580</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2014-02, Vol.9 (2), p.e89580-e89580 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1503271627 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Accumulation Acid resistance Acidification Amino acids Analysis Bioengineering Biology Biosynthesis Carboxylic acids Carboxylic Acids - metabolism Cell Membrane - metabolism Chemicals Computer engineering Cyclopropane Damage detection DNA binding proteins E coli Engineering Escherichia coli Escherichia coli - metabolism Escherichia coli Proteins - metabolism Ethanol Fatty acids Gene expression Gene Expression Regulation, Bacterial Genomes Glutamate Homeostasis Inorganic acids Intracellular Lipids Metabolism Microbiology Octanoic acid pH effects Plasmids Protonmotive force Saturated fatty acids Supplementation Supplements Toxicity Transcription factors |
| title | Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-17T09%3A58%3A13IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Transcriptomic%20analysis%20of%20carboxylic%20acid%20challenge%20in%20Escherichia%20coli:%20beyond%20membrane%20damage&rft.jtitle=PloS%20one&rft.au=Royce,%20Liam%20A&rft.date=2014-02-28&rft.volume=9&rft.issue=2&rft.spage=e89580&rft.epage=e89580&rft.pages=e89580-e89580&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0089580&rft_dat=%3Cgale_plos_%3EA478787742%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1503271627&rft_id=info:pmid/24586888&rft_galeid=A478787742&rft_doaj_id=oai_doaj_org_article_7d7c720b0634472e9e80fbcd4f29b44a&rfr_iscdi=true |