Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms
All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts...
Saved in:
| Published in | iScience Vol. 19; pp. 1133 - 1144 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
27.09.2019
Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2589-0042 2589-0042 |
| DOI | 10.1016/j.isci.2019.08.047 |
Cover
Loading…
| Abstract | All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress.
[Display omitted]
•Characterization of immediate metabolic response to oxidative stress•The metabolic response in glycolysis and PP pathway depends on stress severity•Identification of NADPH feedback inhibition on G6PDH as key regulatory interaction•The identified oxidative stress regulatory interaction is conserved across kingdoms
Biological Sciences; Metabolism; Systems Biology; Metabolic Flux Analysis; Metabolomics; Computational Biology; Bioinformatics |
|---|---|
| AbstractList | All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. : Biological Sciences; Metabolism; Systems Biology; Metabolic Flux Analysis; Metabolomics; Computational Biology; Bioinformatics Subject Areas: Biological Sciences, Metabolism, Systems Biology, Metabolic Flux Analysis, Metabolomics, Computational Biology, Bioinformatics All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress.All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli , yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. • Characterization of immediate metabolic response to oxidative stress • The metabolic response in glycolysis and PP pathway depends on stress severity • Identification of NADPH feedback inhibition on G6PDH as key regulatory interaction • The identified oxidative stress regulatory interaction is conserved across kingdoms Biological Sciences; Metabolism; Systems Biology; Metabolic Flux Analysis; Metabolomics; Computational Biology; Bioinformatics All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. [Display omitted] •Characterization of immediate metabolic response to oxidative stress•The metabolic response in glycolysis and PP pathway depends on stress severity•Identification of NADPH feedback inhibition on G6PDH as key regulatory interaction•The identified oxidative stress regulatory interaction is conserved across kingdoms Biological Sciences; Metabolism; Systems Biology; Metabolic Flux Analysis; Metabolomics; Computational Biology; Bioinformatics |
| Author | Estermann, Alexandra Sauer, Uwe Kuehne, Andreas Lang, Paul Christodoulou, Dimitris Fuhrer, Tobias |
| AuthorAffiliation | 2 Systems Biology Graduate School, Zurich 8057, Switzerland 1 Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland |
| AuthorAffiliation_xml | – name: 1 Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland – name: 2 Systems Biology Graduate School, Zurich 8057, Switzerland |
| Author_xml | – sequence: 1 givenname: Dimitris surname: Christodoulou fullname: Christodoulou, Dimitris organization: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland – sequence: 2 givenname: Andreas surname: Kuehne fullname: Kuehne, Andreas organization: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland – sequence: 3 givenname: Alexandra surname: Estermann fullname: Estermann, Alexandra organization: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland – sequence: 4 givenname: Tobias surname: Fuhrer fullname: Fuhrer, Tobias organization: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland – sequence: 5 givenname: Paul surname: Lang fullname: Lang, Paul organization: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland – sequence: 6 givenname: Uwe surname: Sauer fullname: Sauer, Uwe email: sauer@imsb.biol.ethz.ch organization: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31536961$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9Ul1vEzEQtFAR_aB_gAfkR15y2Oc7ny0hpBJaGlFBheDZ8tl7OUcXO7Uvgfx7nKRFLQ-VLK21OzMr7cwpOvLBA0JvKCkoofz9onDJuKIkVBZEFKRqXqCTshZyQkhVHj36H6PzlBaEkDK_SvJX6JjRmnHJ6QmyPyBB3AC-GtZ_8FSvtHHjFjuPxx7wLfgxpFz7kFa9HvNPj_1vvcXtFn-7-Hx7jT85b52f41nC0-D3WhZrE0NK-Gse2LBMr9HLTg8Jzu_rGfp1dflzej25-f5lNr24mZialM2Ed8KwsmadNoKRlta85rwRBBpZE84tNbLuuDCVAd20TUPbylaya03LteGkZWdodtC1QS_UKrqljlsVtFP7RohzpePozACKalO3BDppaVVZW2neSdMwyzowLHey1seD1mrdLsGafImohyeiTyfe9WoeNooLRoVgWeDdvUAMd2tIo1pmx2AYtIewTqosZV01pOQ0Q98-3vVvyYNNGSAOgP1dI3Qqu6RHF3ar3aAoUbtQqIXahULtQqGIUDkUmVr-R31Qf5b04UCC7NbGQVQZAd6AdRHMmM_pnqP_BeT10NY |
| CitedBy_id | crossref_primary_10_1016_j_freeradbiomed_2025_03_030 crossref_primary_10_1016_j_freeradbiomed_2023_06_021 crossref_primary_10_1016_j_freeradbiomed_2022_10_302 crossref_primary_10_1038_s42003_022_04156_4 crossref_primary_10_1146_annurev_biophys_030722_021957 crossref_primary_10_1128_jvi_01363_22 crossref_primary_10_3390_ijms232214479 crossref_primary_10_1002_mnfr_202100400 crossref_primary_10_1038_s41467_023_44098_x crossref_primary_10_1186_s12934_023_02123_0 crossref_primary_10_3390_pr8080893 crossref_primary_10_1016_j_micres_2024_127955 crossref_primary_10_3390_fermentation10030166 crossref_primary_10_1038_s42255_022_00550_8 crossref_primary_10_1002_adma_202109726 crossref_primary_10_3390_jcm11082177 crossref_primary_10_1016_j_isci_2022_104681 crossref_primary_10_1016_j_rbc_2025_100049 crossref_primary_10_1080_13510002_2021_1966183 crossref_primary_10_3390_microorganisms12010112 crossref_primary_10_1038_s42255_023_00863_2 crossref_primary_10_1016_j_celrep_2020_01_013 crossref_primary_10_1016_j_freeradbiomed_2025_03_006 crossref_primary_10_1038_s42255_023_00781_3 crossref_primary_10_1107_S2053230X22001091 crossref_primary_10_1038_s41467_023_42364_6 crossref_primary_10_1038_s42255_021_00523_3 crossref_primary_10_1002_ptr_7045 crossref_primary_10_1016_j_cbd_2021_100946 crossref_primary_10_1016_j_cels_2021_04_009 crossref_primary_10_1016_j_isci_2020_101880 crossref_primary_10_1021_acs_analchem_9b05709 crossref_primary_10_1038_s41589_022_01091_7 crossref_primary_10_1016_j_isci_2021_102753 crossref_primary_10_1016_j_rbmo_2023_01_005 crossref_primary_10_1038_s41598_021_94585_8 crossref_primary_10_1016_j_coisb_2021_100390 crossref_primary_10_1038_s41396_020_00884_9 crossref_primary_10_1161_CIRCULATIONAHA_124_067876 crossref_primary_10_1016_j_chemosphere_2021_131373 |
| Cites_doi | 10.1016/0378-4274(95)03570-2 10.1038/nchembio.2077 10.1128/JB.187.5.1581-1590.2005 10.1146/annurev-pharmtox-011112-140320 10.1146/annurev.biochem.77.061606.161055 10.1128/JB.01523-08 10.1093/nar/gkw1092 10.3109/10715761003667554 10.1016/j.cellsig.2012.01.008 10.1096/fj.00-0074com 10.1038/nrd4002 10.1038/msb.2013.11 10.1042/bj2490293 10.1038/nbt0709-604 10.1126/science.1118439 10.1074/jbc.273.35.22480 10.1111/brv.12140 10.1007/s00203-006-0153-1 10.1016/S0899-9007(02)00916-4 10.1074/jbc.274.38.27002 10.1038/nbt.1499 10.1016/j.cels.2018.04.009 10.1016/j.abb.2012.04.014 10.1074/jbc.M311657200 10.1042/bj20030414 10.1021/ac201267k 10.1021/ac100101d 10.1016/j.redox.2015.09.005 10.1016/S1353-8020(02)00018-4 10.1016/j.celrep.2017.08.066 10.1111/j.1567-1364.2010.00713.x 10.1515/BC.2003.064 10.1523/JNEUROSCI.20-24-08972.2000 10.1080/01926230290166724 10.1085/jgp.201210772 10.1038/cr.2010.178 10.1098/rstb.2005.1764 10.1097/01.WCB.0000050065.57184.BB 10.1002/jcp.10119 10.1186/1477-3163-5-14 10.1111/1574-6976.12026 10.1016/S0955-0674(03)00002-4 10.1038/nbt.2489 10.1161/01.HYP.25.2.155 10.1126/science.1211485 10.1016/j.cels.2015.09.008 10.1038/nrmicro3032 10.1093/nar/28.1.27 10.1016/j.molcel.2015.06.017 10.1128/JB.01795-06 10.1073/pnas.78.11.7124 |
| ContentType | Journal Article |
| Copyright | 2019 The Author(s) Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved. 2019 The Author(s) 2019 |
| Copyright_xml | – notice: 2019 The Author(s) – notice: Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved. – notice: 2019 The Author(s) 2019 |
| DBID | 6I. AAFTH AAYXX CITATION NPM 7X8 5PM DOA |
| DOI | 10.1016/j.isci.2019.08.047 |
| DatabaseName | ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef PubMed MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef PubMed MEDLINE - Academic |
| DatabaseTitleList | PubMed MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Open Access Full Text url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| EISSN | 2589-0042 |
| EndPage | 1144 |
| ExternalDocumentID | oai_doaj_org_article_1ac5b0ef9d144dd4a6f9c73d3fec344d PMC6831883 31536961 10_1016_j_isci_2019_08_047 S2589004219303256 |
| Genre | Journal Article |
| GroupedDBID | 0SF 53G 6I. AACTN AAEDW AAFTH AALRI AAXUO ABMAC ADBBV AEXQZ AFTJW AITUG ALMA_UNASSIGNED_HOLDINGS AMRAJ AOIJS BCNDV EBS EJD FDB GROUPED_DOAJ HYE M41 NCXOZ OK1 ROL RPM SSZ 0R~ AAMRU AAYWO AAYXX ACVFH ADCNI ADVLN AEUPX AFPUW AIGII AKBMS AKYEP APXCP CITATION NPM 7X8 5PM |
| ID | FETCH-LOGICAL-c5027-6f8c3253fac830b156566780e795066d1c95f68c4cea7b771b4d49fbcb6ac60b3 |
| IEDL.DBID | DOA |
| ISSN | 2589-0042 |
| IngestDate | Wed Aug 27 01:22:12 EDT 2025 Thu Aug 21 18:01:26 EDT 2025 Fri Jul 11 03:52:38 EDT 2025 Thu Apr 03 06:58:59 EDT 2025 Thu Apr 24 23:11:09 EDT 2025 Tue Jul 01 01:03:26 EDT 2025 Tue May 16 22:28:48 EDT 2023 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | Biological Sciences Metabolomics Computational Biology Metabolism Metabolic Flux Analysis Systems Biology Bioinformatics |
| Language | English |
| License | This is an open access article under the CC BY license. Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c5027-6f8c3253fac830b156566780e795066d1c95f68c4cea7b771b4d49fbcb6ac60b3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Lead Contact These authors contributed equally |
| OpenAccessLink | https://doaj.org/article/1ac5b0ef9d144dd4a6f9c73d3fec344d |
| PMID | 31536961 |
| PQID | 2295470261 |
| PQPubID | 23479 |
| PageCount | 12 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_1ac5b0ef9d144dd4a6f9c73d3fec344d pubmedcentral_primary_oai_pubmedcentral_nih_gov_6831883 proquest_miscellaneous_2295470261 pubmed_primary_31536961 crossref_citationtrail_10_1016_j_isci_2019_08_047 crossref_primary_10_1016_j_isci_2019_08_047 elsevier_sciencedirect_doi_10_1016_j_isci_2019_08_047 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2019-09-27 |
| PublicationDateYYYYMMDD | 2019-09-27 |
| PublicationDate_xml | – month: 09 year: 2019 text: 2019-09-27 day: 27 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | iScience |
| PublicationTitleAlternate | iScience |
| PublicationYear | 2019 |
| Publisher | Elsevier Inc Elsevier |
| Publisher_xml | – name: Elsevier Inc – name: Elsevier |
| References | Fang, Yang, Wu (bib11) 2002; 18 Dan Dunn, Alvarez, Zhang, Soldati (bib9) 2015; 6 Miyamoto, Koh, Park, Fujiwara, Sakiyama, Misonou, Ookawara, Suzuki, Honke, Taniguchi (bib38) 2003; 384 Imlay (bib21) 2013; 11 Kohen, Nyska (bib26) 2002; 30 Finkel (bib12) 2003; 15 Colussi, Albertini, Coppola, Rovidati, Galli, Ghibelli (bib8) 2000; 14 Ray, Huang, Tsuji (bib45) 2012; 24 Kanehisa, Furumichi, Tanabe, Sato, Morishima (bib25) 2017; 45 Link, Kochanowski, Sauer (bib29) 2013; 31 Kuehne, Emmert, Soehle, Winnefeld, Fischer, Wenck, Gallinat, Terstegen, Lucius, Hildebrand, Zamboni (bib27) 2015; 59 Liu, He, Yao (bib31) 2018; 2018 Murakami, Tsubouchi, Fukayama, Ogawa, Yoshino (bib40) 2006; 186 Shenton, Grant (bib51) 2003; 374 Liou, Storz (bib30) 2010; 44 Zhang, Wang, Vikash, Ye, Wu, Liu, Dong (bib61) 2016; 2016 Waris, Ahsan (bib58) 2006; 5 Raymond, Segrè (bib46) 2006; 311 Christen, Sauer (bib6) 2011; 11 Buescher, Moco, Sauer, Zamboni (bib4) 2010; 82 Ralser, Wamelink, Kowald, Gerisch, Heeren, Struys, Klipp, Jakobs, Breitenbach, Lehrach, Krobitsch (bib43) 2007; 6 Anastasiou, Poulogiannis, Asara, Boxer, Jiang, Shen, Bellinger, Sasaki, Locasale, Auld (bib2) 2011; 334 Fuhrer, Sauer (bib13) 2009; 191 Mytilineou, Kramer, Yabut (bib41) 2002; 8 Inoue, Matsuda, Sugiyama, Izawa, Kimura (bib22) 1999; 274 Reznik, Christodoulou, Goldford, Briars, Sauer, Segrè, Noor (bib47) 2017; 20 Sandoval, Arenas, Vásquez (bib49) 2011; 6 Fuhrer, Heer, Begemann, Zamboni (bib15) 2011; 83 Vatansever, de Melo, Avci, Vecchio, Sadasivam, Gupta, Chandran, Karimi, Parizotto, Yin (bib57) 2013; 37 Chechik, Oh, Rando, Weissman, Regev, Koller (bib5) 2008; 26 Zeller, Kümmel, Ewald, Jol, Niebel, Picotti, Aebersold, Sauer, Zamboni, Heinemann (bib60) 2007; 189 Imlay (bib20) 2008; 77 Christodoulou, Link, Fuhrer, Kochanowski, Gerosa, Sauer (bib7) 2018; 6 Turkheimer, Hinz, Cunningham (bib56) 2003; 23 Gorrini, Harris, Mak (bib18) 2013; 12 Fuhrer, Fischer, Sauer (bib14) 2005; 187 Alexander (bib1) 1995; 25 Lemons, Feng, Bennett, Legesse-Miller, Johnson, Raitman, Pollina, Rabitz, Rabinowitz, Coller (bib28) 2010; 8 Gerosa, Haverkorn van Rijsewijk, Christodoulou, Kochanowski, Schmidt, Noor, Sauer (bib16) 2015; 1 Morgan, Liu (bib39) 2011; 21 Ralser, Wamelink, Latkolik, Jansen, Lehrach, Jakobs (bib44) 2009; 27 Doroshow (bib10) 1995; 82–83 Llobell, Lopez-Ruiz, Peinado, Lopez-Barea (bib32) 1988; 249 Tretter, Adam-Vizi (bib55) 2005; 360 Park, Rubin, Xu, Amador-Noguez, Fan, Shlomi, Rabinowitz (bib42) 2016; 12 Godon, Lagniel, Lee, Buhler, Kieffer, Perrot, Boucherie, Toledano, Labarre (bib17) 1998; 273 Martindale, Holbrook (bib35) 2002; 192 Rui, Shen, Zhou, Liu, Chen, Pan, Liu, Wu, Zheng, Shi (bib48) 2010; 55 Stincone, Prigione, Cramer, Wamelink, Campbell, Cheung, Olin-Sandoval, Grüning, Krüger, Tauqeer Alam (bib52) 2015; 90 Harman (bib19) 1981; 78 Zampar, Kümmel, Ewald, Jol, Niebel, Picotti, Aebersold, Sauer, Zamboni, Heinemann (bib59) 2014; 9 Messiha, Kent, Malys, Carroll, Swainston, Mendes, Smallbone (bib36) 2014 Sauer, Canonaco, Heri, Perrenoud, Fischer (bib50) 2004; 279 Tretter, Adam-Vizi (bib54) 2000; 20 Aon, Stanley, Sivakumaran, Kembro, O'Rourke, Paolocci, Cortassa (bib3) 2012; 139 Ma (bib34) 2013; 53 Kanehisa, Goto (bib24) 2000; 28 Mishra, Imlay (bib37) 2012; 525 Lemons (10.1016/j.isci.2019.08.047_bib28) 2010; 8 Gorrini (10.1016/j.isci.2019.08.047_bib18) 2013; 12 Mishra (10.1016/j.isci.2019.08.047_bib37) 2012; 525 Anastasiou (10.1016/j.isci.2019.08.047_bib2) 2011; 334 Link (10.1016/j.isci.2019.08.047_bib29) 2013; 31 Murakami (10.1016/j.isci.2019.08.047_bib40) 2006; 186 Finkel (10.1016/j.isci.2019.08.047_bib12) 2003; 15 Chechik (10.1016/j.isci.2019.08.047_bib5) 2008; 26 Kanehisa (10.1016/j.isci.2019.08.047_bib25) 2017; 45 Messiha (10.1016/j.isci.2019.08.047_bib36) 2014 Martindale (10.1016/j.isci.2019.08.047_bib35) 2002; 192 Zhang (10.1016/j.isci.2019.08.047_bib61) 2016; 2016 Sauer (10.1016/j.isci.2019.08.047_bib50) 2004; 279 Zampar (10.1016/j.isci.2019.08.047_bib59) 2014; 9 Fuhrer (10.1016/j.isci.2019.08.047_bib13) 2009; 191 Tretter (10.1016/j.isci.2019.08.047_bib54) 2000; 20 Christodoulou (10.1016/j.isci.2019.08.047_bib7) 2018; 6 Aon (10.1016/j.isci.2019.08.047_bib3) 2012; 139 Alexander (10.1016/j.isci.2019.08.047_bib1) 1995; 25 Buescher (10.1016/j.isci.2019.08.047_bib4) 2010; 82 Fuhrer (10.1016/j.isci.2019.08.047_bib14) 2005; 187 Liu (10.1016/j.isci.2019.08.047_bib31) 2018; 2018 Ralser (10.1016/j.isci.2019.08.047_bib43) 2007; 6 Harman (10.1016/j.isci.2019.08.047_bib19) 1981; 78 Liou (10.1016/j.isci.2019.08.047_bib30) 2010; 44 Dan Dunn (10.1016/j.isci.2019.08.047_bib9) 2015; 6 Tretter (10.1016/j.isci.2019.08.047_bib55) 2005; 360 Reznik (10.1016/j.isci.2019.08.047_bib47) 2017; 20 Waris (10.1016/j.isci.2019.08.047_bib58) 2006; 5 Doroshow (10.1016/j.isci.2019.08.047_bib10) 1995; 82–83 Fuhrer (10.1016/j.isci.2019.08.047_bib15) 2011; 83 Ray (10.1016/j.isci.2019.08.047_bib45) 2012; 24 Sandoval (10.1016/j.isci.2019.08.047_bib49) 2011; 6 Ma (10.1016/j.isci.2019.08.047_bib34) 2013; 53 Park (10.1016/j.isci.2019.08.047_bib42) 2016; 12 Morgan (10.1016/j.isci.2019.08.047_bib39) 2011; 21 Rui (10.1016/j.isci.2019.08.047_bib48) 2010; 55 Miyamoto (10.1016/j.isci.2019.08.047_bib38) 2003; 384 Christen (10.1016/j.isci.2019.08.047_bib6) 2011; 11 Stincone (10.1016/j.isci.2019.08.047_bib52) 2015; 90 Zeller (10.1016/j.isci.2019.08.047_bib60) 2007; 189 Vatansever (10.1016/j.isci.2019.08.047_bib57) 2013; 37 Kuehne (10.1016/j.isci.2019.08.047_bib27) 2015; 59 Ralser (10.1016/j.isci.2019.08.047_bib44) 2009; 27 Imlay (10.1016/j.isci.2019.08.047_bib20) 2008; 77 Gerosa (10.1016/j.isci.2019.08.047_bib16) 2015; 1 Mytilineou (10.1016/j.isci.2019.08.047_bib41) 2002; 8 Raymond (10.1016/j.isci.2019.08.047_bib46) 2006; 311 Godon (10.1016/j.isci.2019.08.047_bib17) 1998; 273 Llobell (10.1016/j.isci.2019.08.047_bib32) 1988; 249 Inoue (10.1016/j.isci.2019.08.047_bib22) 1999; 274 Fang (10.1016/j.isci.2019.08.047_bib11) 2002; 18 Kanehisa (10.1016/j.isci.2019.08.047_bib24) 2000; 28 Turkheimer (10.1016/j.isci.2019.08.047_bib56) 2003; 23 Imlay (10.1016/j.isci.2019.08.047_bib21) 2013; 11 Colussi (10.1016/j.isci.2019.08.047_bib8) 2000; 14 Kohen (10.1016/j.isci.2019.08.047_bib26) 2002; 30 Shenton (10.1016/j.isci.2019.08.047_bib51) 2003; 374 |
| References_xml | – volume: 30 start-page: 620 year: 2002 end-page: 650 ident: bib26 article-title: Oxidation of biological systems: oxidative stress phenomena, antioxidants, redox reactions, and methods for their quantification publication-title: Toxicol. Pathol. – volume: 311 start-page: 1764 year: 2006 end-page: 1767 ident: bib46 article-title: The effect of oxygen on biochemical networks and the evolution of complex life publication-title: Science – volume: 20 start-page: 8972 year: 2000 end-page: 8979 ident: bib54 article-title: Inhibition of Krebs cycle enzymes by hydrogen peroxide: a key role of [alpha]-ketoglutarate dehydrogenase in limiting NADH production under oxidative stress publication-title: J. Neurosci. – volume: 14 start-page: 2266 year: 2000 end-page: 2276 ident: bib8 article-title: H2O2-induced block of glycolysis as an active ADP-ribosylation reaction protecting cells from apoptosis publication-title: FASEB J. – volume: 55 start-page: 831 year: 2010 end-page: 840 ident: bib48 article-title: A systematic investigation of publication-title: BMC Syst. Biol. – volume: 12 start-page: 931 year: 2013 end-page: 947 ident: bib18 article-title: Modulation of oxidative stress as an anticancer strategy publication-title: Nat. Rev. Drug Discov. – volume: 11 start-page: 443 year: 2013 end-page: 454 ident: bib21 article-title: The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium publication-title: Nat. Rev. Microbiol. – volume: 1 start-page: 270 year: 2015 end-page: 282 ident: bib16 article-title: Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data publication-title: Cell Syst. – volume: 82–83 start-page: 395 year: 1995 end-page: 398 ident: bib10 article-title: Glutathione peroxidase and oxidative stress publication-title: Toxicol. Lett. – volume: 31 start-page: 357 year: 2013 end-page: 361 ident: bib29 article-title: Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo publication-title: Nat. Biotechnol. – volume: 24 start-page: 981 year: 2012 end-page: 990 ident: bib45 article-title: Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling publication-title: Cell Signal. – volume: 6 start-page: 569 year: 2018 end-page: 578.e7 ident: bib7 article-title: Reserve flux capacity in the pentose phosphate pathway enables publication-title: Cell Syst. – volume: 44 start-page: 479 year: 2010 end-page: 496 ident: bib30 article-title: Reactive oxygen species in cancer publication-title: Free Radic. Res. – volume: 59 start-page: 359 year: 2015 end-page: 371 ident: bib27 article-title: Acute activation of oxidative pentose phosphate pathway as first-line response to oxidative stress in human skin cells publication-title: Mol. Cell – volume: 82 start-page: 4403 year: 2010 end-page: 4412 ident: bib4 article-title: Ultrahigh performance liquid chromatography−tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites publication-title: Anal. Chem. – volume: 139 start-page: 479 year: 2012 end-page: 491 ident: bib3 article-title: Glutathione/thioredoxin systems modulate mitochondrial H publication-title: J. Gen. Physiol. – volume: 374 start-page: 513 year: 2003 end-page: 519 ident: bib51 article-title: Protein S-thiolation targets glycolysis and protein synthesis in response to oxidative stress in the yeast publication-title: Biochem. J. – volume: 189 start-page: 3784 year: 2007 end-page: 3792 ident: bib60 article-title: Regulation of hydrogen peroxide-dependent gene expression in publication-title: J. Bacteriol. – volume: 15 start-page: 247 year: 2003 end-page: 254 ident: bib12 article-title: Oxidant signals and oxidative stress publication-title: Curr. Opin. Cell Biol. – volume: 27 start-page: 604 year: 2009 end-page: 605 ident: bib44 article-title: Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response publication-title: Nat. Biotechnol. – volume: 6 start-page: 472 year: 2015 end-page: 485 ident: bib9 article-title: Reactive oxygen species and mitochondria: a nexus of cellular homeostasis publication-title: Redox Biol. – volume: 21 start-page: 103 year: 2011 end-page: 115 ident: bib39 article-title: Crosstalk of reactive oxygen species and NF-κB signaling publication-title: Cell Res. – volume: 53 start-page: 401 year: 2013 end-page: 426 ident: bib34 article-title: Role of Nrf2 in oxidative stress and toxicity publication-title: Annu. Rev. Pharmacol. Toxicol. – volume: 26 start-page: 1251 year: 2008 end-page: 1259 ident: bib5 article-title: Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network publication-title: Nat. Biotechnol. – volume: 77 start-page: 755 year: 2008 end-page: 776 ident: bib20 article-title: Cellular defenses against superoxide and hydrogen peroxide publication-title: Annu. Rev. Biochem. – volume: 525 start-page: 145 year: 2012 end-page: 160 ident: bib37 article-title: Why do bacteria use so many enzymes to scavenge hydrogen peroxide? publication-title: Arch. Biochem. Biophys. – volume: 5 start-page: 14 year: 2006 ident: bib58 article-title: Reactive oxygen species: role in the development of cancer and various chronic conditions publication-title: J. Carcinog. – volume: 384 start-page: 567 year: 2003 end-page: 574 ident: bib38 article-title: Oxidative stress caused by inactivation of glutathione peroxidase and adaptive responses publication-title: Biol. Chem. – volume: 249 start-page: 293 year: 1988 end-page: 296 ident: bib32 article-title: Glutathione reductase directly mediates the stimulation of yeast glucose-6-phosphate dehydrogenase by GSSG publication-title: Biochem. J. – volume: 186 start-page: 385 year: 2006 end-page: 392 ident: bib40 article-title: Oxidative inactivation of reduced NADP-generating enzymes in publication-title: Arch. Microbiol. – volume: 274 start-page: 27002 year: 1999 end-page: 27009 ident: bib22 article-title: Genetic analysis of glutathione peroxidase in oxidative stress response of publication-title: J. Biol. Chem. – volume: 90 start-page: 927 year: 2015 end-page: 963 ident: bib52 article-title: The return of metabolism: biochemistry and physiology of the pentose phosphate pathway publication-title: Biol. Rev. – volume: 360 start-page: 2335 year: 2005 end-page: 2345 ident: bib55 article-title: Alpha-ketoglutarate dehydrogenase: a target and generator of oxidative stress publication-title: Philos. Trans. R. Soc. B Biol. Sci. – volume: 2016 start-page: 1 year: 2016 end-page: 18 ident: bib61 article-title: ROS and ROS-mediated cellular signaling publication-title: Oxid. Med. Cell Longev. – volume: 83 start-page: 7074 year: 2011 end-page: 7080 ident: bib15 article-title: High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection–time-of-flight mass spectrometry publication-title: Anal. Chem. – volume: 191 start-page: 2112 year: 2009 end-page: 2121 ident: bib13 article-title: Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism publication-title: J. Bacteriol. – volume: 78 start-page: 7124 year: 1981 end-page: 7128 ident: bib19 article-title: The aging process publication-title: Proc. Natl. Acad. Sci. U S A – volume: 11 start-page: 263 year: 2011 end-page: 272 ident: bib6 article-title: Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics publication-title: FEMS Yeast Res. – volume: 273 start-page: 22480 year: 1998 end-page: 22489 ident: bib17 article-title: The H2O2 stimulon in publication-title: J. Biol. Chem. – volume: 28 start-page: 27 year: 2000 end-page: 30 ident: bib24 article-title: KEGG: Kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res. – volume: 9 start-page: 651 year: 2014 ident: bib59 article-title: Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast publication-title: Mol. Syst. Biol. – volume: 279 start-page: 6613 year: 2004 end-page: 6619 ident: bib50 article-title: The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of publication-title: J. Biol. Chem. – volume: 45 start-page: D353 year: 2017 end-page: D361 ident: bib25 article-title: KEGG: new perspectives on genomes, pathways, diseases and drugs publication-title: Nucleic Acids Res. – volume: 23 start-page: 490 year: 2003 end-page: 498 ident: bib56 article-title: On the undecidability among kinetic models: from model selection to model averaging publication-title: J. Cereb. Blood Flow Metab. – volume: 187 start-page: 1581 year: 2005 end-page: 1590 ident: bib14 article-title: Experimental identification and quantification of glucose metabolism in seven bacterial species publication-title: J. Bacteriol. – year: 2014 ident: bib36 article-title: Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast publication-title: PeerJ Inc. – volume: 192 start-page: 1 year: 2002 end-page: 15 ident: bib35 article-title: Cellular response to oxidative stress: signaling for suicide and survival publication-title: J. Cell Physiol. – volume: 20 start-page: 2666 year: 2017 end-page: 2677 ident: bib47 article-title: Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity publication-title: Cell Rep. – volume: 6 start-page: 10 year: 2007 ident: bib43 article-title: Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress publication-title: J. Biol. – volume: 12 start-page: 482 year: 2016 end-page: 489 ident: bib42 article-title: Metabolite concentrations, fluxes and free energies imply efficient enzyme usage publication-title: Nat. Chem. Biol. – volume: 2018 start-page: 3408467 year: 2018 ident: bib31 article-title: The antioxidative function of alpha-ketoglutarate and its applications publication-title: Biomed. Res. Int. – volume: 8 start-page: 385 year: 2002 end-page: 387 ident: bib41 article-title: Glutathione depletion and oxidative stress publication-title: Parkinsonism Relat. Disord. – volume: 6 start-page: e25573 year: 2011 ident: bib49 article-title: Glucose-6-Phosphate dehydrogenase protects publication-title: PLoS One – volume: 8 start-page: e1000514 year: 2010 ident: bib28 article-title: Quiescent fibroblasts exhibit high metabolic activity publication-title: PLoS Biology – volume: 334 start-page: 1278 year: 2011 end-page: 1283 ident: bib2 article-title: Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses publication-title: Science – volume: 37 start-page: 955 year: 2013 end-page: 989 ident: bib57 article-title: Antimicrobial strategies centered around reactive oxygen species – bactericidal antibiotics, photodynamic therapy, and beyond publication-title: FEMS Microbiol. Rev. – volume: 25 start-page: 155 year: 1995 end-page: 161 ident: bib1 article-title: Theodore Cooper Memorial Lecture. Hypertension and the pathogenesis of atherosclerosis. Oxidative stress and the mediation of arterial inflammatory response: a new perspective publication-title: Hypertension – volume: 18 start-page: 872 year: 2002 end-page: 879 ident: bib11 article-title: Free radicals, antioxidants, and nutrition publication-title: Nutrition – volume: 82–83 start-page: 395 year: 1995 ident: 10.1016/j.isci.2019.08.047_bib10 article-title: Glutathione peroxidase and oxidative stress publication-title: Toxicol. Lett. doi: 10.1016/0378-4274(95)03570-2 – volume: 12 start-page: 482 year: 2016 ident: 10.1016/j.isci.2019.08.047_bib42 article-title: Metabolite concentrations, fluxes and free energies imply efficient enzyme usage publication-title: Nat. Chem. Biol. doi: 10.1038/nchembio.2077 – volume: 6 start-page: e25573 year: 2011 ident: 10.1016/j.isci.2019.08.047_bib49 article-title: Glucose-6-Phosphate dehydrogenase protects Escherichia coli from tellurite-mediated oxidative stress – volume: 187 start-page: 1581 year: 2005 ident: 10.1016/j.isci.2019.08.047_bib14 article-title: Experimental identification and quantification of glucose metabolism in seven bacterial species publication-title: J. Bacteriol. doi: 10.1128/JB.187.5.1581-1590.2005 – volume: 53 start-page: 401 year: 2013 ident: 10.1016/j.isci.2019.08.047_bib34 article-title: Role of Nrf2 in oxidative stress and toxicity publication-title: Annu. Rev. Pharmacol. Toxicol. doi: 10.1146/annurev-pharmtox-011112-140320 – volume: 77 start-page: 755 year: 2008 ident: 10.1016/j.isci.2019.08.047_bib20 article-title: Cellular defenses against superoxide and hydrogen peroxide publication-title: Annu. Rev. Biochem. doi: 10.1146/annurev.biochem.77.061606.161055 – volume: 191 start-page: 2112 year: 2009 ident: 10.1016/j.isci.2019.08.047_bib13 article-title: Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism publication-title: J. Bacteriol. doi: 10.1128/JB.01523-08 – volume: 45 start-page: D353 year: 2017 ident: 10.1016/j.isci.2019.08.047_bib25 article-title: KEGG: new perspectives on genomes, pathways, diseases and drugs publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw1092 – volume: 44 start-page: 479 year: 2010 ident: 10.1016/j.isci.2019.08.047_bib30 article-title: Reactive oxygen species in cancer publication-title: Free Radic. Res. doi: 10.3109/10715761003667554 – volume: 24 start-page: 981 year: 2012 ident: 10.1016/j.isci.2019.08.047_bib45 article-title: Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling publication-title: Cell Signal. doi: 10.1016/j.cellsig.2012.01.008 – volume: 14 start-page: 2266 year: 2000 ident: 10.1016/j.isci.2019.08.047_bib8 article-title: H2O2-induced block of glycolysis as an active ADP-ribosylation reaction protecting cells from apoptosis publication-title: FASEB J. doi: 10.1096/fj.00-0074com – volume: 12 start-page: 931 year: 2013 ident: 10.1016/j.isci.2019.08.047_bib18 article-title: Modulation of oxidative stress as an anticancer strategy publication-title: Nat. Rev. Drug Discov. doi: 10.1038/nrd4002 – volume: 2018 start-page: 3408467 year: 2018 ident: 10.1016/j.isci.2019.08.047_bib31 article-title: The antioxidative function of alpha-ketoglutarate and its applications publication-title: Biomed. Res. Int. – volume: 9 start-page: 651 year: 2014 ident: 10.1016/j.isci.2019.08.047_bib59 article-title: Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast publication-title: Mol. Syst. Biol. doi: 10.1038/msb.2013.11 – volume: 249 start-page: 293 year: 1988 ident: 10.1016/j.isci.2019.08.047_bib32 article-title: Glutathione reductase directly mediates the stimulation of yeast glucose-6-phosphate dehydrogenase by GSSG publication-title: Biochem. J. doi: 10.1042/bj2490293 – volume: 27 start-page: 604 year: 2009 ident: 10.1016/j.isci.2019.08.047_bib44 article-title: Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response publication-title: Nat. Biotechnol. doi: 10.1038/nbt0709-604 – volume: 311 start-page: 1764 year: 2006 ident: 10.1016/j.isci.2019.08.047_bib46 article-title: The effect of oxygen on biochemical networks and the evolution of complex life publication-title: Science doi: 10.1126/science.1118439 – volume: 273 start-page: 22480 year: 1998 ident: 10.1016/j.isci.2019.08.047_bib17 article-title: The H2O2 stimulon in Saccharomyces cerevisiae publication-title: J. Biol. Chem. doi: 10.1074/jbc.273.35.22480 – volume: 90 start-page: 927 year: 2015 ident: 10.1016/j.isci.2019.08.047_bib52 article-title: The return of metabolism: biochemistry and physiology of the pentose phosphate pathway publication-title: Biol. Rev. doi: 10.1111/brv.12140 – volume: 186 start-page: 385 year: 2006 ident: 10.1016/j.isci.2019.08.047_bib40 article-title: Oxidative inactivation of reduced NADP-generating enzymes in E. coli: iron-dependent inactivation with affinity cleavage of NADP-isocitrate dehydrogenase publication-title: Arch. Microbiol. doi: 10.1007/s00203-006-0153-1 – volume: 2016 start-page: 1 year: 2016 ident: 10.1016/j.isci.2019.08.047_bib61 article-title: ROS and ROS-mediated cellular signaling publication-title: Oxid. Med. Cell Longev. – volume: 18 start-page: 872 year: 2002 ident: 10.1016/j.isci.2019.08.047_bib11 article-title: Free radicals, antioxidants, and nutrition publication-title: Nutrition doi: 10.1016/S0899-9007(02)00916-4 – volume: 274 start-page: 27002 year: 1999 ident: 10.1016/j.isci.2019.08.047_bib22 article-title: Genetic analysis of glutathione peroxidase in oxidative stress response of Saccharomyces cerevisiae publication-title: J. Biol. Chem. doi: 10.1074/jbc.274.38.27002 – volume: 26 start-page: 1251 year: 2008 ident: 10.1016/j.isci.2019.08.047_bib5 article-title: Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1499 – volume: 55 start-page: 831 year: 2010 ident: 10.1016/j.isci.2019.08.047_bib48 article-title: A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress publication-title: BMC Syst. Biol. – volume: 6 start-page: 569 year: 2018 ident: 10.1016/j.isci.2019.08.047_bib7 article-title: Reserve flux capacity in the pentose phosphate pathway enables Escherichia coli’s rapid response to oxidative stress publication-title: Cell Syst. doi: 10.1016/j.cels.2018.04.009 – volume: 525 start-page: 145 year: 2012 ident: 10.1016/j.isci.2019.08.047_bib37 article-title: Why do bacteria use so many enzymes to scavenge hydrogen peroxide? publication-title: Arch. Biochem. Biophys. doi: 10.1016/j.abb.2012.04.014 – volume: 6 start-page: 10 year: 2007 ident: 10.1016/j.isci.2019.08.047_bib43 article-title: Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress publication-title: J. Biol. – volume: 279 start-page: 6613 year: 2004 ident: 10.1016/j.isci.2019.08.047_bib50 article-title: The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli publication-title: J. Biol. Chem. doi: 10.1074/jbc.M311657200 – volume: 374 start-page: 513 issue: Pt 2 year: 2003 ident: 10.1016/j.isci.2019.08.047_bib51 article-title: Protein S-thiolation targets glycolysis and protein synthesis in response to oxidative stress in the yeast Saccharomyces cerevisiae publication-title: Biochem. J. doi: 10.1042/bj20030414 – volume: 83 start-page: 7074 year: 2011 ident: 10.1016/j.isci.2019.08.047_bib15 article-title: High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection–time-of-flight mass spectrometry publication-title: Anal. Chem. doi: 10.1021/ac201267k – volume: 82 start-page: 4403 year: 2010 ident: 10.1016/j.isci.2019.08.047_bib4 article-title: Ultrahigh performance liquid chromatography−tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites publication-title: Anal. Chem. doi: 10.1021/ac100101d – volume: 6 start-page: 472 year: 2015 ident: 10.1016/j.isci.2019.08.047_bib9 article-title: Reactive oxygen species and mitochondria: a nexus of cellular homeostasis publication-title: Redox Biol. doi: 10.1016/j.redox.2015.09.005 – volume: 8 start-page: 385 year: 2002 ident: 10.1016/j.isci.2019.08.047_bib41 article-title: Glutathione depletion and oxidative stress publication-title: Parkinsonism Relat. Disord. doi: 10.1016/S1353-8020(02)00018-4 – volume: 20 start-page: 2666 year: 2017 ident: 10.1016/j.isci.2019.08.047_bib47 article-title: Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity publication-title: Cell Rep. doi: 10.1016/j.celrep.2017.08.066 – volume: 8 start-page: e1000514 year: 2010 ident: 10.1016/j.isci.2019.08.047_bib28 article-title: Quiescent fibroblasts exhibit high metabolic activity – volume: 11 start-page: 263 year: 2011 ident: 10.1016/j.isci.2019.08.047_bib6 article-title: Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics publication-title: FEMS Yeast Res. doi: 10.1111/j.1567-1364.2010.00713.x – volume: 384 start-page: 567 year: 2003 ident: 10.1016/j.isci.2019.08.047_bib38 article-title: Oxidative stress caused by inactivation of glutathione peroxidase and adaptive responses publication-title: Biol. Chem. doi: 10.1515/BC.2003.064 – volume: 20 start-page: 8972 year: 2000 ident: 10.1016/j.isci.2019.08.047_bib54 article-title: Inhibition of Krebs cycle enzymes by hydrogen peroxide: a key role of [alpha]-ketoglutarate dehydrogenase in limiting NADH production under oxidative stress publication-title: J. Neurosci. doi: 10.1523/JNEUROSCI.20-24-08972.2000 – volume: 30 start-page: 620 year: 2002 ident: 10.1016/j.isci.2019.08.047_bib26 article-title: Oxidation of biological systems: oxidative stress phenomena, antioxidants, redox reactions, and methods for their quantification publication-title: Toxicol. Pathol. doi: 10.1080/01926230290166724 – volume: 139 start-page: 479 year: 2012 ident: 10.1016/j.isci.2019.08.047_bib3 article-title: Glutathione/thioredoxin systems modulate mitochondrial H2O2 emission: an experimental-computational study publication-title: J. Gen. Physiol. doi: 10.1085/jgp.201210772 – volume: 21 start-page: 103 year: 2011 ident: 10.1016/j.isci.2019.08.047_bib39 article-title: Crosstalk of reactive oxygen species and NF-κB signaling publication-title: Cell Res. doi: 10.1038/cr.2010.178 – volume: 360 start-page: 2335 year: 2005 ident: 10.1016/j.isci.2019.08.047_bib55 article-title: Alpha-ketoglutarate dehydrogenase: a target and generator of oxidative stress publication-title: Philos. Trans. R. Soc. B Biol. Sci. doi: 10.1098/rstb.2005.1764 – year: 2014 ident: 10.1016/j.isci.2019.08.047_bib36 article-title: Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast publication-title: PeerJ Inc. – volume: 23 start-page: 490 year: 2003 ident: 10.1016/j.isci.2019.08.047_bib56 article-title: On the undecidability among kinetic models: from model selection to model averaging publication-title: J. Cereb. Blood Flow Metab. doi: 10.1097/01.WCB.0000050065.57184.BB – volume: 192 start-page: 1 year: 2002 ident: 10.1016/j.isci.2019.08.047_bib35 article-title: Cellular response to oxidative stress: signaling for suicide and survival publication-title: J. Cell Physiol. doi: 10.1002/jcp.10119 – volume: 5 start-page: 14 year: 2006 ident: 10.1016/j.isci.2019.08.047_bib58 article-title: Reactive oxygen species: role in the development of cancer and various chronic conditions publication-title: J. Carcinog. doi: 10.1186/1477-3163-5-14 – volume: 37 start-page: 955 year: 2013 ident: 10.1016/j.isci.2019.08.047_bib57 article-title: Antimicrobial strategies centered around reactive oxygen species – bactericidal antibiotics, photodynamic therapy, and beyond publication-title: FEMS Microbiol. Rev. doi: 10.1111/1574-6976.12026 – volume: 15 start-page: 247 year: 2003 ident: 10.1016/j.isci.2019.08.047_bib12 article-title: Oxidant signals and oxidative stress publication-title: Curr. Opin. Cell Biol. doi: 10.1016/S0955-0674(03)00002-4 – volume: 31 start-page: 357 year: 2013 ident: 10.1016/j.isci.2019.08.047_bib29 article-title: Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2489 – volume: 25 start-page: 155 year: 1995 ident: 10.1016/j.isci.2019.08.047_bib1 article-title: Theodore Cooper Memorial Lecture. Hypertension and the pathogenesis of atherosclerosis. Oxidative stress and the mediation of arterial inflammatory response: a new perspective publication-title: Hypertension doi: 10.1161/01.HYP.25.2.155 – volume: 334 start-page: 1278 year: 2011 ident: 10.1016/j.isci.2019.08.047_bib2 article-title: Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses publication-title: Science doi: 10.1126/science.1211485 – volume: 1 start-page: 270 year: 2015 ident: 10.1016/j.isci.2019.08.047_bib16 article-title: Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data publication-title: Cell Syst. doi: 10.1016/j.cels.2015.09.008 – volume: 11 start-page: 443 year: 2013 ident: 10.1016/j.isci.2019.08.047_bib21 article-title: The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro3032 – volume: 28 start-page: 27 year: 2000 ident: 10.1016/j.isci.2019.08.047_bib24 article-title: KEGG: Kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.1.27 – volume: 59 start-page: 359 year: 2015 ident: 10.1016/j.isci.2019.08.047_bib27 article-title: Acute activation of oxidative pentose phosphate pathway as first-line response to oxidative stress in human skin cells publication-title: Mol. Cell doi: 10.1016/j.molcel.2015.06.017 – volume: 189 start-page: 3784 year: 2007 ident: 10.1016/j.isci.2019.08.047_bib60 article-title: Regulation of hydrogen peroxide-dependent gene expression in Rhodobacter sphaeroides: regulatory functions of OxyR publication-title: J. Bacteriol. doi: 10.1128/JB.01795-06 – volume: 78 start-page: 7124 year: 1981 ident: 10.1016/j.isci.2019.08.047_bib19 article-title: The aging process publication-title: Proc. Natl. Acad. Sci. U S A doi: 10.1073/pnas.78.11.7124 |
| SSID | ssj0002002496 |
| Score | 2.3014796 |
| Snippet | All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved... All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved... |
| SourceID | doaj pubmedcentral proquest pubmed crossref elsevier |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 1133 |
| SubjectTerms | Bioinformatics Biological Sciences Computational Biology Metabolic Flux Analysis Metabolism Metabolomics Systems Biology |
| Title | Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms |
| URI | https://dx.doi.org/10.1016/j.isci.2019.08.047 https://www.ncbi.nlm.nih.gov/pubmed/31536961 https://www.proquest.com/docview/2295470261 https://pubmed.ncbi.nlm.nih.gov/PMC6831883 https://doaj.org/article/1ac5b0ef9d144dd4a6f9c73d3fec344d |
| Volume | 19 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Nb9QwELVQT70gELQsFGQkblVEHNtxfGwLq4VDtYdW6s3yp3arklRNF-i_Z8bJrnapVC6cIiWO48lMMs_y-D1CPjFntatiLLSvYiGcFIW2rCpsHRiXjVPWZbbP83p2Kb5fyastqS-sCRvogYcX95lZL10Zkw4A_UMQtk7aKx54ip7DGfz7Qs7bmkxd5-U1pMLLynISa4IgNMcdM0NxF-54xbounfk7UVtlKytl8v6d5PQYfP5dQ7mVlKYvyPMRTdKTwYqX5FlsX5GA1XR3PyOd3qx-0zPIhh6gNl22FMAenUNPXQ_HRdffLgBp0jmAwF_2gboHen7yZT6jp8u81YV-6ynqeWJfgdo8cooaKKH70b8ml9OvF2ezYhRTKLyEqWdRp8bzSvJkfcNLxzKQU00ZlZYAOwLzWqa68cJHq5xSzIkgdHLe1dbXpeMHZK_t2viG0IYhaUxKlS-TUOAP7ZxVXgeugw-MTQhbv0zjR6ZxFLy4MeuSsmuDDjDoAIMqmEJNyPHmntuBZ-PJ1qfoo01L5MjOJyByzBg55l-RMyFy7WEzwo0BRkBXyycf_nEdDga-RVxgsW3sVr1BaXShcFY7IYdDeGyGyCG11BqvqJ3A2bFh90q7XGS-77qBH2_D3_4Po9-RfTQFK14qdUT27u9W8T3Aqnv3IX9BfwD3ECFu |
| linkProvider | Directory of Open Access Journals |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Reserve+Flux+Capacity+in+the+Pentose+Phosphate+Pathway+by+NADPH+Binding+Is+Conserved+across+Kingdoms&rft.jtitle=iScience&rft.au=Christodoulou%2C+Dimitris&rft.au=Kuehne%2C+Andreas&rft.au=Estermann%2C+Alexandra&rft.au=Fuhrer%2C+Tobias&rft.date=2019-09-27&rft.eissn=2589-0042&rft.volume=19&rft.spage=1133&rft_id=info:doi/10.1016%2Fj.isci.2019.08.047&rft_id=info%3Apmid%2F31536961&rft.externalDocID=31536961 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2589-0042&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2589-0042&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2589-0042&client=summon |