{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T08:59:46Z","timestamp":1769849986644,"version":"3.49.0"},"reference-count":64,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    The efficient conversion of lignocellulosic sugars into bioethanol is constrained by the inability of\n                    <jats:italic>Saccharomyces cerevisiae<\/jats:italic>\n                    to metabolize xylose and by its preference for glucose when both sugars are available. Although recombinant strains have been developed to improve xylose utilization, further optimization is needed to achieve robust co-fermentation performance. In this study, three parental strains were used: a wild-type\n                    <jats:italic>S. cerevisiae<\/jats:italic>\n                    strain (GF16), a genetically engineered\n                    <jats:italic>S. cerevisiae<\/jats:italic>\n                    strain capable of metabolizing xylose (TMB3001), and a reference strain of\n                    <jats:italic>Scheffersomyces stipitis<\/jats:italic>\n                    (ATCC 58376). From these, we obtained an evolved\n                    <jats:italic>S. cerevisiae<\/jats:italic>\n                    strain (F2C7A) through a combination of UV mutagenesis, protoplast fusion, and adaptive laboratory evolution. In synthetic medium containing only xylose, F2C7A consumed 87.9% of the sugar after 72 h, compared with only 52.3% by its parental hybrid strain, although, its biomass yield was lower (0.20 g\/g vs. 0.35 g\/g). Under mixed-sugar conditions, F2C7A consumed all available glucose and 33% of xylose within 48 h, producing ethanol at 0.45 g\/g yield with minimal xylitol accumulation. In culture medium containing only xylose, it reached a biomass yield of 0.86 g\/g and a xylitol yield of 0.11 g\/g. Transcriptomic analysis revealed strong induction of\n                    <jats:italic>XYL1<\/jats:italic>\n                    ,\n                    <jats:italic>XYL2<\/jats:italic>\n                    , tricarboxylic acid cycle genes, and oxidative phosphorylation components under xylose, consistent with a respiratory phenotype. Mixed-sugar cultures displayed a respirofermentative profile and reduced xylitol formation, suggesting improved redox balance in the presence of glucose. Several nonspecific sugar transporters (\n                    <jats:italic>HXT8<\/jats:italic>\n                    ,\n                    <jats:italic>HGT1<\/jats:italic>\n                    ,\n                    <jats:italic>STL1<\/jats:italic>\n                    ) were overexpressed under xylose, indicating potential compensatory uptake mechanisms. Changes in nitrogen metabolism included upregulation of\n                    <jats:italic>GLT1<\/jats:italic>\n                    and repression of\n                    <jats:italic>GDH1<\/jats:italic>\n                    , suggesting a shift toward NADH-dependent glutamate synthesis. These findings demonstrate that combining classical and evolutionary strategies can enhance xylose metabolism in\n                    <jats:italic>S. cerevisiae<\/jats:italic>\n                    , providing a foundation for further improvement of strains intended for lignocellulosic bioethanol production.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0341927","type":"journal-article","created":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T18:38:13Z","timestamp":1769798293000},"page":"e0341927","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Adaptive laboratory evolution and transcriptomic profiling reveal carbon\u2013nitrogen metabolic reprogramming enabling aerobic co-fermentation of glucose and xylose in Saccharomyces cerevisiae"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0099-6261","authenticated-orcid":true,"given":"Lina Maria","family":"L\u00f3pez-de\u00c1vila","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0583-8086","authenticated-orcid":true,"given":"Zulma Isabel","family":"Monsalve-Fonnegra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1413-9022","authenticated-orcid":true,"given":"H\u00e9ctor Alejandro","family":"Rodr\u00edguez-Cabal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,1,30]]},"reference":[{"key":"pone.0341927.ref001","doi-asserted-by":"crossref","first-page":"129926","DOI":"10.1016\/j.biortech.2023.129926","article-title":"Utilization of agricultural wastes for co-production of xylitol, ethanol, and phenylacetylcarbinol: A review","volume":"392","author":"J Feng","year":"2024","journal-title":"Bioresour Technol"},{"key":"pone.0341927.ref002","doi-asserted-by":"crossref","first-page":"104239","DOI":"10.1016\/j.seta.2025.104239","article-title":"Sustainable biorefinery approaches in the valorization of agro-food industrial residues for biofuel production: Economic and future perspectives","volume":"75","author":"YP Ragini","year":"2025","journal-title":"Sustainable Energy Technologies and Assessments"},{"issue":"10","key":"pone.0341927.ref003","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.3390\/molecules29102275","article-title":"Composition of Lignocellulose Hydrolysate in Different Biorefinery Strategies: Nutrients and Inhibitors","volume":"29","author":"Y Wang","year":"2024","journal-title":"Molecules"},{"issue":"1","key":"pone.0341927.ref004","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1080\/21655979.2020.1801178","article-title":"Engineered Saccharomyces cerevisiae for lignocellulosic valorization: a review and perspectives on bioethanol production","volume":"11","author":"JT Cunha","year":"2020","journal-title":"Bioengineered"},{"issue":"1","key":"pone.0341927.ref005","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/s12934-017-0766-x","article-title":"Comparative assessment of fermentative capacity of different xylose-consuming yeasts","volume":"16","author":"HCT Veras","year":"2017","journal-title":"Microb Cell Fact"},{"issue":"8","key":"pone.0341927.ref006","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1128\/AEM.66.8.3381-3386.2000","article-title":"Anaerobic xylose fermentation by recombinant Saccharomyces cerevisiae carrying XYL1, XYL2, and XKS1 in mineral medium chemostat cultures","volume":"66","author":"A Eliasson","year":"2000","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"pone.0341927.ref007","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1016\/j.femsyr.2004.01.003","article-title":"Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of principle","volume":"4","author":"M Kuyper","year":"2004","journal-title":"FEMS Yeast Res"},{"issue":"1","key":"pone.0341927.ref008","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.enzmictec.2012.03.008","article-title":"Characterization of non-oxidative transaldolase and transketolase enzymes in the pentose phosphate pathway with regard to xylose utilization by recombinant Saccharomyces cerevisiae","volume":"51","author":"A Matsushika","year":"2012","journal-title":"Enzyme Microb Technol"},{"issue":"1","key":"pone.0341927.ref009","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s12934-019-1141-x","article-title":"Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants","volume":"18","author":"KO Osiro","year":"2019","journal-title":"Microb Cell Fact"},{"issue":"22","key":"pone.0341927.ref010","doi-asserted-by":"crossref","first-page":"12410","DOI":"10.3390\/ijms222212410","article-title":"D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers","volume":"22","author":"DP Brink","year":"2021","journal-title":"Int J Mol Sci"},{"issue":"2","key":"pone.0341927.ref011","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/s10123-018-00044-2","article-title":"Improved ethanol productivity and ethanol tolerance through genome shuffling of Saccharomyces cerevisiae and Pichia stipitis","volume":"22","author":"KD Jetti","year":"2019","journal-title":"Int Microbiol"},{"key":"pone.0341927.ref012"},{"issue":"2","key":"pone.0341927.ref013","article-title":"Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae","volume":"8","author":"SR Kim","year":"2013","journal-title":"PLoS One"},{"key":"pone.0341927.ref014","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.procbio.2020.05.022","article-title":"Construction of industrial xylose-fermenting Saccharomyces cerevisiae strains through combined approaches","volume":"96","author":"C-Y Xie","year":"2020","journal-title":"Process Biochemistry"},{"issue":"8","key":"pone.0341927.ref015","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.3390\/microorganisms12081526","article-title":"Development of a Robust Saccharomyces cerevisiae Strain for Efficient Co-Fermentation of Mixed Sugars and Enhanced Inhibitor Tolerance through Protoplast Fusion","volume":"12","author":"J Zhao","year":"2024","journal-title":"Microorganisms"},{"key":"pone.0341927.ref016","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.procbio.2020.12.022","article-title":"Improving multiple stress-tolerance of a flocculating industrial Saccharomyces cerevisiae strain by random mutagenesis and hybridization","volume":"102","author":"L Wang","year":"2021","journal-title":"Process Biochemistry"},{"key":"pone.0341927.ref017","doi-asserted-by":"crossref","DOI":"10.1093\/femsyr\/foaf004","article-title":"Experimental evolution and hybridization enhance the fermentative capacity of wild Saccharomyces eubayanus strains","volume":"25","author":"F Vega-Macaya","year":"2025","journal-title":"FEMS Yeast Res"},{"issue":"8","key":"pone.0341927.ref018","doi-asserted-by":"crossref","first-page":"2266","DOI":"10.1111\/1751-7915.14068","article-title":"Generation of intra- and interspecific Saccharomyces hybrids with improved oenological and aromatic properties","volume":"15","author":"D P\u00e9rez","year":"2022","journal-title":"Microb Biotechnol"},{"issue":"3","key":"pone.0341927.ref019","first-page":"277","article-title":"The non-oxidative pentose phosphate pathway controls the fermentation rate of xylulose but not of xylose in Saccharomyces cerevisiae TMB3001","volume":"2","author":"B Johansson","year":"2002","journal-title":"FEMS Yeast Res"},{"key":"pone.0341927.ref020","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s13068-015-0239-6","article-title":"Evolved strains of Scheffersomyces stipitis achieving high ethanol productivity on acid- and base-pretreated biomass hydrolyzate at high solids loading","volume":"8","author":"PJ Slininger","year":"2015","journal-title":"Biotechnol Biofuels"},{"key":"pone.0341927.ref021","article-title":"EMS and UV mutagenesis in yeast","author":"F Winston","year":"2008","journal-title":"Curr Protoc Mol Biol"},{"issue":"6","key":"pone.0341927.ref022","doi-asserted-by":"crossref","first-page":"2591","DOI":"10.1007\/s00253-011-3693-5","article-title":"Improved inhibitor tolerance in xylose-fermenting yeast Spathaspora passalidarum by mutagenesis and protoplast fusion","volume":"93","author":"X Hou","year":"2012","journal-title":"Appl Microbiol Biotechnol"},{"key":"pone.0341927.ref023","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.mimet.2016.06.012","article-title":"Genome shuffling of Saccharomyces cerevisiae for enhanced glutathione yield and relative gene expression analysis using fluorescent quantitation reverse transcription polymerase chain reaction","volume":"127","author":"H Yin","year":"2016","journal-title":"J Microbiol Methods"},{"issue":"5","key":"pone.0341927.ref024","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1007\/s10295-011-1076-7","article-title":"A genome shuffling-generated Saccharomyces cerevisiae isolate that ferments xylose and glucose to produce high levels of ethanol","volume":"39","author":"G Jingping","year":"2012","journal-title":"J Ind Microbiol Biotechnol"},{"issue":"09","key":"pone.0341927.ref025","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1042\/BSR20253121","article-title":"Improvement of autochthonous Saccharomyces cerevisiae by rapid laboratory evolution technique of genome shuffling","volume":"45","author":"R Hospet","year":"2025","journal-title":"Bioscience Reports"},{"issue":"1","key":"pone.0341927.ref026","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00294-016-0609-z","article-title":"Reprogramming of nonfermentative metabolism by stress-responsive transcription factors in the yeast Saccharomyces cerevisiae","volume":"63","author":"N Soontorngun","year":"2017","journal-title":"Curr Genet"},{"issue":"16","key":"pone.0341927.ref027","doi-asserted-by":"crossref","first-page":"3580","DOI":"10.3390\/molecules25163580","article-title":"Chinese Yellow Rice Wine Processing with Reduced Ethyl Carbamate Formation by Deleting Transcriptional Regulator Dal80p in Saccharomyces cerevisiae","volume":"25","author":"T Wei","year":"2020","journal-title":"Molecules"},{"issue":"24","key":"pone.0341927.ref028","doi-asserted-by":"crossref","first-page":"8392","DOI":"10.1128\/AEM.02056-15","article-title":"Improvement of glucose uptake rate and production of target chemicals by overexpressing hexose transporters and transcriptional activator Gcr1 in Saccharomyces cerevisiae","volume":"81","author":"D Kim","year":"2015","journal-title":"Appl Environ Microbiol"},{"issue":"9","key":"pone.0341927.ref029","doi-asserted-by":"crossref","first-page":"4027","DOI":"10.1007\/s00253-020-10518-x","article-title":"Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy","volume":"104","author":"JA Bubis","year":"2020","journal-title":"Appl Microbiol Biotechnol"},{"key":"pone.0341927.ref030","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/978-3-319-25304-6_6","article-title":"Sugar and Glycerol Transport in Saccharomyces cerevisiae","volume":"892","author":"LF Bisson","year":"2016","journal-title":"Adv Exp Med Biol"},{"issue":"4","key":"pone.0341927.ref031","doi-asserted-by":"crossref","DOI":"10.1093\/femsyr\/foab026","article-title":"Identification of novel pentose transporters in Kluyveromyces marxianus using a new screening platform","volume":"21","author":"L Donzella","year":"2021","journal-title":"FEMS Yeast Res"},{"issue":"2","key":"pone.0341927.ref032","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jbiotec.2008.03.009","article-title":"In vivo regulation of glucose transporter genes at glucose concentrations between 0 and 500 mg\/L in a wild type of Saccharomyces cerevisiae","volume":"135","author":"C Klockow","year":"2008","journal-title":"J Biotechnol"},{"issue":"4","key":"pone.0341927.ref033","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1128\/MMBR.00022-12","article-title":"Evolutionary role of interspecies hybridization and genetic exchanges in yeasts","volume":"76","author":"L Morales","year":"2012","journal-title":"Microbiol Mol Biol Rev"},{"key":"pone.0341927.ref034","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/yea.3684","article-title":"Saccharomyces yeast hybrids on the rise","volume":"39","author":"DP Bendixsen","year":"2022","journal-title":"Yeast"},{"issue":"9","key":"pone.0341927.ref035","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1007\/s00122-023-04436-5","article-title":"Maximization through optimization? On the relationship between hybrid performance and parental genetic distance","volume":"136","author":"T W\u00fcrschum","year":"2023","journal-title":"Theor Appl Genet"},{"issue":"14","key":"pone.0341927.ref036","doi-asserted-by":"crossref","first-page":"6331","DOI":"10.1007\/s00253-016-7481-0","article-title":"Genotypic and phenotypic evolution of yeast interspecies hybrids during high-sugar fermentation","volume":"100","author":"K Lopandic","year":"2016","journal-title":"Appl Microbiol Biotechnol"},{"issue":"8","key":"pone.0341927.ref037","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1007\/s12010-021-03539-3","article-title":"Strain Improvement of Native Saccharomyces cerevisiae LN ITCC 8246 Strain Through Protoplast Fusion To Enhance Its Xylose Uptake","volume":"193","author":"S Sharma","year":"2021","journal-title":"Appl Biochem Biotechnol"},{"issue":"9","key":"pone.0341927.ref038","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1002\/yea.3429","article-title":"d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review","volume":"36","author":"MA Pati\u00f1o","year":"2019","journal-title":"Yeast"},{"key":"pone.0341927.ref039","doi-asserted-by":"crossref","first-page":"107795","DOI":"10.1016\/j.biotechadv.2021.107795","article-title":"Adaptive laboratory evolution principles and applications in industrial biotechnology","volume":"54","author":"M Mavrommati","year":"2022","journal-title":"Biotechnol Adv"},{"issue":"2","key":"pone.0341927.ref040","doi-asserted-by":"crossref","first-page":"186","DOI":"10.3390\/jof9020186","article-title":"Contributions of Adaptive Laboratory Evolution towards the Enhancement of the Biotechnological Potential of Non-Conventional Yeast Species","volume":"9","author":"T Fernandes","year":"2023","journal-title":"J Fungi (Basel)"},{"issue":"2","key":"pone.0341927.ref041","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1134\/S0003683821020198","article-title":"Improvement of Acetic Acid Tolerance in Saccharomyces cerevisiae by Novel Genome Shuffling","volume":"57","author":"A Wawro","year":"2021","journal-title":"Appl Biochem Microbiol"},{"key":"pone.0341927.ref042","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/s13068-017-0887-9","article-title":"Saccharomyces cerevisiae strain comparison in glucose-xylose fermentations on defined substrates and in high-gravity SSCF: convergence in strain performance despite differences in genetic and evolutionary engineering history","volume":"10","author":"V Novy","year":"2017","journal-title":"Biotechnol Biofuels"},{"key":"pone.0341927.ref043","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1007\/s10295-020-02281-9","article-title":"Improvement in D-xylose utilization and isobutanol production in S. cerevisiae by adaptive laboratory evolution and rational engineering","volume":"47","author":"P Promdonkoy","year":"2020","journal-title":"J Ind Microbiol Biotechnol"},{"issue":"1","key":"pone.0341927.ref044","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/1754-6834-6-151","article-title":"Adaptive evolution of an industrial strain of Saccharomyces cerevisiae for combined tolerance to inhibitors and temperature","volume":"6","author":"V Wallace-Salinas","year":"2013","journal-title":"Biotechnol Biofuels"},{"issue":"11","key":"pone.0341927.ref045","doi-asserted-by":"crossref","first-page":"6816","DOI":"10.1128\/AEM.70.11.6816-6825.2004","article-title":"Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response","volume":"70","author":"Y-S Jin","year":"2004","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"pone.0341927.ref046","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1111\/1567-1364.12153","article-title":"Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology","volume":"14","author":"JL Mart\u00ednez","year":"2014","journal-title":"FEMS Yeast Res"},{"issue":"2","key":"pone.0341927.ref047","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1007\/s00253-015-7038-7","article-title":"Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures","volume":"100","author":"S Alff-Tuomala","year":"2016","journal-title":"Appl Microbiol Biotechnol"},{"issue":"3","key":"pone.0341927.ref048","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1007\/s12010-012-0013-1","article-title":"Characterization of a recombinant flocculent Saccharomyces cerevisiae strain that co-ferments glucose and xylose: I. Influence of the ratio of glucose\/xylose on ethanol production","volume":"169","author":"A Matsushika","year":"2013","journal-title":"Appl Biochem Biotechnol"},{"issue":"9","key":"pone.0341927.ref049","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1016\/j.procbio.2012.05.004","article-title":"Consolidated bioprocessing and simultaneous saccharification and fermentation of lignocellulose to ethanol with thermotolerant yeast strains","volume":"47","author":"T Hasunuma","year":"2012","journal-title":"Process Biochemistry"},{"issue":"8","key":"pone.0341927.ref050","doi-asserted-by":"crossref","first-page":"130154","DOI":"10.1016\/j.bbagen.2022.130154","article-title":"Xylose and yeasts: A story beyond xylitol production","volume":"1866","author":"AK Estrada-\u00c1vila","year":"2022","journal-title":"Biochim Biophys Acta Gen Subj"},{"issue":"1","key":"pone.0341927.ref051","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/s42770-024-01564-y","article-title":"Xylitol bioproduction by Candida tropicalis: effects of glucose\/xylose ratio and pH on fermentation and gene expression","volume":"56","author":"SS Queiroz","year":"2025","journal-title":"Braz J Microbiol"},{"issue":"7","key":"pone.0341927.ref052","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1002\/jctb.1570","article-title":"Effect of glucose:xylose ratio on xylose reductase and xylitol dehydrogenase activities from Candida guilliermondii in sugarcane bagasse hydrolysate","volume":"81","author":"DDV da Silva","year":"2006","journal-title":"J of Chemical Tech & Biotech"},{"issue":"3","key":"pone.0341927.ref053","article-title":"Development and genomic elucidation of hybrid yeast with improved glucose-xylose co-fermentation at high temperature","volume":"19","author":"Y Lin","year":"2019","journal-title":"FEMS Yeast Res"},{"issue":"5","key":"pone.0341927.ref054","doi-asserted-by":"crossref","first-page":"450","DOI":"10.3390\/fermentation9050450","article-title":"Optimization Conditions for Ethanol Production from Sweet Sorghum Juice by Thermotolerant Yeast Saccharomyces cerevisiae: Using a Statistical Experimental Design","volume":"9","author":"S Nuanpeng","year":"2023","journal-title":"Fermentation"},{"issue":"1","key":"pone.0341927.ref055","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13068-023-02320-4","article-title":"D-xylose accelerated death of pentose metabolizing Saccharomyces cerevisiae","volume":"16","author":"JG Nijland","year":"2023","journal-title":"Biotechnol Biofuels Bioprod"},{"issue":"3","key":"pone.0341927.ref056","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/s41589-024-01771-6","article-title":"Engineering a xylose fermenting yeast for lignocellulosic ethanol production","volume":"21","author":"Y-W Zhang","year":"2025","journal-title":"Nat Chem Biol"},{"issue":"5","key":"pone.0341927.ref057","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1007\/s00253-006-0747-1","article-title":"Xylose transport studies with xylose-utilizing Saccharomyces cerevisiae strains expressing heterologous and homologous permeases","volume":"74","author":"A Saloheimo","year":"2007","journal-title":"Appl Microbiol Biotechnol"},{"issue":"11","key":"pone.0341927.ref058","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.00095-17","article-title":"Improved Xylose Metabolism by a CYC8 Mutant of Saccharomyces cerevisiae","volume":"83","author":"JG Nijland","year":"2017","journal-title":"Appl Environ Microbiol"},{"key":"pone.0341927.ref059","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/s13068-015-0360-6","article-title":"An engineered cryptic Hxt11 sugar transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae","volume":"8","author":"HY Shin","year":"2015","journal-title":"Biotechnol Biofuels"},{"issue":"13","key":"pone.0341927.ref060","doi-asserted-by":"crossref","first-page":"4347","DOI":"10.1128\/MCB.21.13.4347-4368.2001","article-title":"Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast","volume":"21","author":"K Natarajan","year":"2001","journal-title":"Mol Cell Biol"},{"issue":"10","key":"pone.0341927.ref061","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0292949","article-title":"Gcn4 impacts metabolic fluxes to promote yeast chronological lifespan","volume":"18","author":"JF Gulias","year":"2023","journal-title":"PLoS One"},{"issue":"11","key":"pone.0341927.ref062","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1038\/cr.2010.146","article-title":"Identifying cooperative transcription factors by combining ChIP-chip data and knockout data","volume":"20","author":"Y Yang","year":"2010","journal-title":"Cell Res"},{"issue":"8","key":"pone.0341927.ref063","doi-asserted-by":"crossref","first-page":"4732","DOI":"10.1128\/AEM.69.8.4732-4736.2003","article-title":"Metabolic engineering of ammonium assimilation in xylose-fermenting Saccharomyces cerevisiae improves ethanol production","volume":"69","author":"C Roca","year":"2003","journal-title":"Appl Environ Microbiol"},{"key":"pone.0341927.ref064","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.ymben.2005.07.003","article-title":"Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains","volume":"7","author":"T Grotkjaer","year":"2005","journal-title":"Metab Eng"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0341927","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T18:38:22Z","timestamp":1769798302000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0341927"}},"subtitle":[],"editor":[{"given":"Kandasamy","family":"Ulaganathan","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,30]]},"references-count":64,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0341927","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,30]]}}}