{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:09:35Z","timestamp":1790096975403,"version":"4.0.1"},"reference-count":32,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"KUSynBio Special Research Incubator Unit"},{"DOI":"10.13039\/501100004539","name":"Kasetsart University Research and Development Institute (KURDI) and the Nordic Alumni Engagement Initiative 2026","doi-asserted-by":"publisher","award":["FF(KU-SRIU)5.69"],"award-info":[{"award-number":["FF(KU-SRIU)5.69"]}],"id":[{"id":"10.13039\/501100004539","id-type":"DOI","asserted-by":"publisher"}]},{"award":["FF(KU-SRIU)5.69"],"award-info":[{"award-number":["FF(KU-SRIU)5.69"]}],"id":[{"id":"https:\/\/ror.org\/01r8yv121","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The green microalga Chlamydomonas reinhardtii holds substantial promise as a photosynthetic cell factory for sustainable bioproduction, yet strain-specific metabolic responses to environmental stress remain underexplored. Here, we reconstructed a genome-scale metabolic network (GSMN) of the light-tolerant strain C. reinhardtii CC-4414 by combining de novo genome assembly with integrative proteomics. The resulting model, designated iYH2021, comprises 2021 genes, 2601 reactions, and 2089 metabolites, representing the first genome-scale metabolic reconstruction reported for this strain. To elucidate light-driven metabolic remodeling, we integrated quantitative proteomic data from high-light (HL) and low-light (LL) conditions into the model using the iMAT algorithm and performed metabolic flux analysis (MFA). Because these context-specific networks integrate only proteomically supported reactions, flux predictions were evaluated using an objective function that captures photon-handling capacity, providing a direct readout of how the photosynthetic apparatus reallocates flux under each condition. Our predictions revealed that HL conditions significantly enhanced fluxes through photosynthetic electron transport, the Calvin\u2013Benson cycle, glycolysis, and the tricarboxylic acid (TCA) cycle, indicating a reallocation of carbon and energy metabolism toward light-driven pathways, while amino acid metabolism showed a mixed pattern of change. In contrast, LL conditions induced a marked upregulation of purine metabolism, suggesting accelerated nucleotide turnover as an adaptive response to light limitation. A complementary growth-rate analysis using the unconstrained network further indicated a higher maximum growth rate under HL than LL, consistent with the expected benefit of greater light availability. These condition-specific flux redistributions highlight the metabolic plasticity of C. reinhardtii CC-4414 and provide a systems-level understanding of how light intensity shapes carbon and energy allocation. The iYH2021 model thus offers a robust predictive platform for guiding metabolic engineering strategies aimed at optimizing the production of biofuels and high-value bioproducts in this industrially relevant microalga under stress conditions. These findings represent model-derived predictions and have not yet been experimentally validated. We emphasize that this predictive platform requires experimental validation before its use in guiding metabolic engineering decisions.<\/jats:p>","DOI":"10.3390\/ijms27188383","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:32:12Z","timestamp":1790083932000},"page":"8383","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Proteomics and Genome-Scale Modeling Elucidate Metabolic Flux Shifts in Chlamydomonas reinhardtii CC-4414 Under Light Stress"],"prefix":"10.3390","volume":"27","author":[{"given":"Kittichai","family":"Yosdee","sequence":"first","affiliation":[{"name":"Kasetsart University International College, Kasetsart University, Bangkok 10900, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Vichugorn","family":"Wattayagorn","sequence":"additional","affiliation":[{"name":"Kasetsart University International College, Kasetsart University, Bangkok 10900, Thailand"},{"name":"KUSynBio Special Research Incubator Unit, Kasetsart University International College (KUIC), Kasetsart University, Bangkok 10900, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Yuke","family":"He","sequence":"additional","affiliation":[{"name":"Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5392-8302","authenticated-orcid":false,"given":"Wanida","family":"Pan-utai","sequence":"additional","affiliation":[{"name":"Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7182-6198","authenticated-orcid":false,"given":"Solange I.","family":"Mussatto","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Biomedicine, Technical University of Denmark, S\u00f8ltofts Plads, Building 223, 2800 Kongens Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3072-1733","authenticated-orcid":false,"given":"Pramote","family":"Chumnanpuen","sequence":"additional","affiliation":[{"name":"KUSynBio Special Research Incubator Unit, Kasetsart University International College (KUIC), Kasetsart University, Bangkok 10900, Thailand"},{"name":"Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Wanwipa","family":"Vongsangnak","sequence":"additional","affiliation":[{"name":"KUSynBio Special Research Incubator Unit, Kasetsart University International College (KUIC), Kasetsart University, Bangkok 10900, Thailand"},{"name":"Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Barkia, I., Saari, N., and Manning, S.R. (2019). Microalgae for high-value products towards human health and nutrition. Mar. Drugs, 17.","DOI":"10.3390\/md17050304"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"296","DOI":"10.3144\/expresspolymlett.2018.27","article-title":"A review of extractions of seaweed hydrocolloids: Properties and applications","volume":"12","author":"Khalil","year":"2018","journal-title":"Express Polym. Lett."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1601","DOI":"10.1534\/genetics.105.044503","article-title":"Portrait of a species: Chlamydomonas reinhardtii","volume":"170","author":"Harris","year":"2005","journal-title":"Genetics"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1111\/tpj.12781","article-title":"Establishing Chlamydomonas reinhardtii as an industrial biotechnology host","volume":"82","author":"Scaife","year":"2015","journal-title":"Plant J."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Darwish, R.M., Magee, K.J., Gedi, M.A., Farmanfarmaian, A., Zaky, A.S., Young, I., and Gray, D.A. (2023). Evaluation of chlamydomonas reinhardtii microalgae as a sustainable feed supplement and fishmeal substitute in aquaculture with a positive impact on human nutrition. Fermentation, 9.","DOI":"10.3390\/fermentation9070682"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1126\/science.1143609","article-title":"The Chlamydomonas genome reveals the evolution of key animal and plant functions","volume":"318","author":"Merchant","year":"2007","journal-title":"Science"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Intha, T., and Sirikhachornkit, A. (2023). Pigment Production of Chlamydomonas Strains in Response to Norflurazon and ZnO Nanoparticles. Fermentation, 9.","DOI":"10.3390\/fermentation9020193"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Suwannachuen, N., Leetanasaksakul, K., Roytrakul, S., Phaonakrop, N., Thaisakun, S., Roongsattham, P., Jantasuriyarat, C., Sanevas, N., and Sirikhachornkit, A. (2023). Palmelloid formation and cell aggregation are essential mechanisms for high light tolerance in a natural strain of Chlamydomonas reinhardtii. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24098374"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s13059-019-1730-3","article-title":"Current status and applications of genome-scale metabolic models","volume":"20","author":"Gu","year":"2019","journal-title":"Genome Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1016\/j.febslet.2010.04.052","article-title":"Use of genome-scale metabolic models for understanding microbial physiology","volume":"584","author":"Liu","year":"2010","journal-title":"FEBS Lett."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1038\/msb.2011.52","article-title":"Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism","volume":"7","author":"Chang","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Gomes de Oliveira Dal\u2019Molin, C., Quek, L.-E., Palfreyman, R.W., and Nielsen, L.K. (2011). AlgaGEM\u2013a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-S4-S5"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1111\/tpj.13059","article-title":"A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses","volume":"84","author":"Imam","year":"2015","journal-title":"Plant J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12934-022-02004-y","article-title":"Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii","volume":"22","author":"Yao","year":"2023","journal-title":"Microb. Cell Fact."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1093\/bioinformatics\/btq602","article-title":"iMAT: An integrative metabolic analysis tool","volume":"26","author":"Zur","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"He, J., Liu, C., Du, M., Zhou, X., Hu, Z., Lei, A., and Wang, J. (2021). Metabolic responses of a model green microalga Euglena gracilis to different environmental stresses. Front. Bioeng. Biotechnol., 9.","DOI":"10.3389\/fbioe.2021.662655"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1007\/s10811-013-9983-9","article-title":"High-value products from microalgae\u2014Their development and commercialisation","volume":"25","author":"Borowitzka","year":"2013","journal-title":"J. Appl. Phycol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.biortech.2017.01.006","article-title":"Microalgae biorefinery: High value products perspectives","volume":"229","author":"Chew","year":"2017","journal-title":"Bioresour. Technol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3103","DOI":"10.1007\/s10811-018-1455-9","article-title":"RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)","volume":"30","author":"Poong","year":"2018","journal-title":"J. Appl. Phycol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"12367","DOI":"10.1021\/acs.energyfuels.5c01676","article-title":"Advances and perspectives of microalgal biorefineries for bioenergy","volume":"39","author":"Choudhary","year":"2025","journal-title":"Energy Fuels"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes de novo assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"D516","DOI":"10.1093\/nar\/gkae987","article-title":"OrthoDB and BUSCO update: Annotation of orthologs with wider sampling of genomes","volume":"53","author":"Tegenfeldt","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1093\/bioinformatics\/btr010","article-title":"A novel hybrid gene prediction method employing protein multiple sequence alignments","volume":"27","author":"Keller","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"304","DOI":"10.12688\/f1000research.23297.1","article-title":"GFF utilities: GffRead and GffCompare","volume":"9","author":"Pertea","year":"2020","journal-title":"F1000Research"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Shen, W., Le, S., Li, Y., and Hu, F. (2016). SeqKit: A cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0163962"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7542","DOI":"10.1093\/nar\/gky537","article-title":"Fast automated reconstruction of genome-scale metabolic models for microbial species and communities","volume":"46","author":"Machado","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Wang, H., Marcisauskas, S., Sanchez, B.J., Domenzain, I., Hermansson, D., Agren, R., Nielsen, J., and Kerkhoven, E.J. (2018). RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput. Biol., 14.","DOI":"10.1101\/321067"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41596-018-0098-2","article-title":"Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0","volume":"14","author":"Heirendt","year":"2019","journal-title":"Nat. Protoc."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8383\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:33:41Z","timestamp":1790094821000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8383"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,20]]},"references-count":32,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27188383"],"URL":"https:\/\/doi.org\/10.3390\/ijms27188383","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,20]]}}}