{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T20:41:29Z","timestamp":1790887289068,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012280","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,8,15]],"date-time":"2024-08-15T00:00:00Z","timestamp":1723680000000}}],"reference-count":74,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T00:00:00Z","timestamp":1722816000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["453048493"],"award-info":[{"award-number":["453048493"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001823","name":"Ministry of Education, Youth and Sports of CR","doi-asserted-by":"crossref","award":["LUAUS24131"],"award-info":[{"award-number":["LUAUS24131"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The metabolism of phototrophic cyanobacteria is an integral part of global biogeochemical cycles, and the capability of cyanobacteria to assimilate atmospheric CO\n                    <jats:sub>2<\/jats:sub>\n                    into organic carbon has manifold potential applications for a sustainable biotechnology. To elucidate the properties of cyanobacterial metabolism and growth, computational reconstructions of genome-scale metabolic networks play an increasingly important role. Here, we present an updated reconstruction of the metabolic network of the cyanobacterium\n                    <jats:italic>Synechocystis<\/jats:italic>\n                    sp. PCC 6803 and its quantitative evaluation using flux balance analysis (FBA). To overcome limitations of conventional FBA, and to allow for the integration of experimental analyses, we develop a novel approach to describe light absorption and light utilization within the framework of FBA. Our approach incorporates photoinhibition and a variable quantum yield into the constraint-based description of light-limited phototrophic growth. We show that the resulting model is capable of predicting quantitative properties of cyanobacterial growth, including photosynthetic oxygen evolution and the ATP\/NADPH ratio required for growth and cellular maintenance. Our approach retains the computational and conceptual simplicity of FBA and is readily applicable to other phototrophic microorganisms.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012280","type":"journal-article","created":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T13:43:05Z","timestamp":1722865385000},"page":"e1012280","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["A quantitative description of light-limited cyanobacterial growth using flux balance analysis"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5259-6470","authenticated-orcid":true,"given":"Rune","family":"H\u00f6per","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daria","family":"Komkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0849-3503","authenticated-orcid":true,"given":"Tom\u00e1\u0161","family":"Zav\u0159el","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2217-1655","authenticated-orcid":true,"given":"Ralf","family":"Steuer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,8,5]]},"reference":[{"key":"pcbi.1012280.ref001","doi-asserted-by":"crossref","first-page":"e42508","DOI":"10.7554\/eLife.42508","article-title":"Quantitative insights into the cyanobacterial cell economy","volume":"8","author":"T Zav\u0159el","year":"2019","journal-title":"eLife"},{"issue":"4","key":"pcbi.1012280.ref002","doi-asserted-by":"crossref","DOI":"10.1042\/BSR20193325","article-title":"Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. 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I. Photoinhibition and D1 protein degradation in vitro and in the absence of chloroplast protein synthesis in vivo","volume":"41","author":"E Tyystj\u00e4rvi","year":"1994","journal-title":"Photosynth Res"},{"issue":"5","key":"pcbi.1012280.ref042","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1073\/pnas.93.5.2213","article-title":"The rate constant of photoinhibition, measured in lincomycin-treated leaves, is directly proportional to light intensity","volume":"93","author":"E Tyystj\u00e4rvi","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"pcbi.1012280.ref043","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/S1360-1385(99)01387-4","article-title":"Photosystem-II damage and repair cycle in chloroplasts: what modulates the rate of photodamage in vivo?","volume":"4","author":"A Melis","year":"1999","journal-title":"Trends in Plant Science"},{"issue":"1","key":"pcbi.1012280.ref044","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.bbabio.2011.04.010","article-title":"Parameterization of photosystem II photoinactivation and repair","volume":"1817","author":"DA Campbell","year":"2012","journal-title":"Biochimica et Biophysica Acta (BBA)\u2014Bioenergetics"},{"issue":"1","key":"pcbi.1012280.ref045","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/s12934-019-1209-7","article-title":"Optimal proteome allocation strategies for phototrophic growth in a light-limited chemostat","volume":"18","author":"M Faizi","year":"2019","journal-title":"Microb Cell Fact"},{"issue":"6","key":"pcbi.1012280.ref046","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1016\/j.ymben.2011.08.002","article-title":"Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis","volume":"13","author":"JD Young","year":"2011","journal-title":"Metab Eng"},{"issue":"1","key":"pcbi.1012280.ref047","doi-asserted-by":"crossref","first-page":"e16278","DOI":"10.1371\/journal.pone.0016278","article-title":"Modulation of the major paths of carbon in photorespiratory mutants of Synechocystis","volume":"6","author":"J Huege","year":"2011","journal-title":"PLoS One"},{"key":"pcbi.1012280.ref048","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ymben.2021.10.012","article-title":"Quantifying the propagation of parametric uncertainty on flux balance analysis","volume":"69","author":"HV Dinh","year":"2022","journal-title":"Metab Eng"},{"issue":"8","key":"pcbi.1012280.ref049","doi-asserted-by":"crossref","first-page":"e1700764","DOI":"10.1002\/biot.201700764","article-title":"Increasing the Photoautotrophic Growth Rate of Synechocystis sp. 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