{"entity": "researcher", "timestamp": "2026-08-13T19:06:56.393Z", "family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "affiliations": ["Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.", "Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0"}}, "publications": [{"entity": "publication", "iuid": "0b47a1ccf6df45f189be4688ab57ff66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b47a1ccf6df45f189be4688ab57ff66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b47a1ccf6df45f189be4688ab57ff66"}}, "title": "Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.", "authors": [{"family": "C\u00e1mara", "given": "Elena", "initials": "E", "orcid": "0000-0003-4271-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b95845cfd0040449c13682905f082d4.json"}}, {"family": "Mormino", "given": "Maurizio", "initials": "M", "orcid": "0000-0003-2055-5081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bfdb794959c4feeb11d6e12d68efc06.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}, {"family": "Nyg\u00e5rd", "given": "Yvonne", "initials": "Y", "orcid": "0000-0001-6117-0343", "researcher": {"href": "https://publications.scilifelab.se/researcher/a136743764bc4dc4aa4d363c5a930592.json"}}], "type": "journal article", "published": "2024-05-21", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "issn-l": "0099-2240", "volume": "90", "issue": "5", "pages": "e0233023"}, "abstract": "Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness.\r\n\r\nThe need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.", "doi": "10.1128/aem.02330-23", "pmid": "38587374", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11107148"}], "notes": [], "created": "2024-11-12T10:46:30.209Z", "modified": "2024-11-12T10:49:33.922Z"}, {"entity": "publication", "iuid": "719491976bd04e65be26e8a423af45d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/719491976bd04e65be26e8a423af45d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/719491976bd04e65be26e8a423af45d3"}}, "title": "Engineering Yeast to Improve Heterologous Abscisic Acid Production", "authors": [{"family": "Otto", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-4380-2439", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb33dff940c64620938a10075913b08e.json"}}, {"family": "Gossing", "given": "Michael", "initials": "M", "orcid": "0000-0001-6794-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c99f63c080e45de8e9f77bc605e7769.json"}}, {"family": "David", "given": "Florian", "initials": "F", "orcid": "0000-0003-1831-1619", "researcher": {"href": "https://publications.scilifelab.se/researcher/aebb8a6c2b8846d49f7a19ecf28ddebf.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}], "type": "posted-content", "published": "2023-06-08", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.06.07.544016", "pmid": null, "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-03T13:11:39.183Z", "modified": "2025-12-18T19:50:51.259Z"}, {"entity": "publication", "iuid": "8a3681268a4e40aab47db2cc786c3441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a3681268a4e40aab47db2cc786c3441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a3681268a4e40aab47db2cc786c3441"}}, "title": "A highly selective cell-based fluorescent biosensor for genistein detection", "authors": [{"family": "Chao", "given": "Lucy Fang I", "initials": "LFI"}, {"family": "Liu", "given": "Dany", "initials": "D", "orcid": "0000-0002-0859-6879", "researcher": {"href": "https://publications.scilifelab.se/researcher/85b1e6347a9c4a9eb0c1a661c2075d8d.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}], "type": "journal-article", "published": "2023-06-00", "journal": {"title": "Engineering Microbiology", "issn": "2667-3703", "volume": "3", "issue": "2", "pages": "100078", "issn-l": null}, "abstract": null, "doi": "10.1016/j.engmic.2023.100078", "pmid": "39629249", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-03T13:11:36.855Z", "modified": "2025-12-03T11:36:36.109Z"}, {"entity": "publication", "iuid": "80598a402d1b433eab6523099ba59e86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80598a402d1b433eab6523099ba59e86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80598a402d1b433eab6523099ba59e86"}}, "title": "Sense and Screen-ability: Development of tuneable, biosensor-based screening platforms for abscisic acid", "authors": [{"family": "Otto", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-4380-2439", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb33dff940c64620938a10075913b08e.json"}}, {"family": "Dabirian", "given": "Yasaman", "initials": "Y", "orcid": "0000-0002-8568-6878", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c04cbab746b426ebb167142bfc44b79.json"}}, {"family": "David", "given": "Florian", "initials": "F", "orcid": "0000-0003-1831-1619", "researcher": {"href": "https://publications.scilifelab.se/researcher/aebb8a6c2b8846d49f7a19ecf28ddebf.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}], "type": "posted-content", "published": "2023-05-18", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.05.16.540971", "pmid": null, "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-03T13:11:41.732Z", "modified": "2025-12-19T07:49:27.842Z"}, {"entity": "publication", "iuid": "f1f9f62fd9604400bd6c0577e660f552", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1f9f62fd9604400bd6c0577e660f552.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1f9f62fd9604400bd6c0577e660f552"}}, "title": "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.", "authors": [{"family": "Domenzain", "given": "Iv\u00e1n", "initials": "I", "orcid": "0000-0002-5322-2040", "researcher": {"href": "https://publications.scilifelab.se/researcher/3793e87625584ee2a31301297263a12a.json"}}, {"family": "S\u00e1nchez", "given": "Benjam\u00edn", "initials": "B", "orcid": "0000-0001-6093-4110", "researcher": {"href": "https://publications.scilifelab.se/researcher/def9067db1624ff49e94cc67ba5d4208.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df361f8014144e79479631fcbffad53.json"}}, {"family": "Mill\u00e1n-Oropeza", "given": "Aar\u00f3n", "initials": "A"}, {"family": "Henry", "given": "C\u00e9line", "initials": "C", "orcid": "0000-0002-2355-1791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf23e6c84ff4fe0a0055f39bcf0b1bf.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}, {"family": "Morrissey", "given": "John P", "initials": "JP", "orcid": "0000-0001-7960-2001", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf59d720c3b34732949d72b0ada6512e.json"}}, {"family": "Sonnenschein", "given": "Nikolaus", "initials": "N"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2022-06-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3766"}, "abstract": "Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.", "doi": "10.1038/s41467-022-31421-1", "pmid": "35773252", "labels": {"Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9246944"}, {"db": "pii", "key": "10.1038/s41467-022-31421-1"}], "notes": [], "created": "2023-05-17T11:26:17.072Z", "modified": "2023-05-17T11:35:04.659Z"}]}