A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications

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dc.contributor.authorPearcy, Nicoleko
dc.contributor.authorGaravaglia, Marcoko
dc.contributor.authorMillat, Thomasko
dc.contributor.authorGilbert, James P.ko
dc.contributor.authorSong, Yosebko
dc.contributor.authorHartman, Hassanko
dc.contributor.authorWoods, Craigko
dc.contributor.authorTomi-Andrino, Claudioko
dc.contributor.authorBommareddy, Rajesh Reddyko
dc.contributor.authorCho, Byung-Kwanko
dc.contributor.authorFell, David A.ko
dc.contributor.authorPoolman, Markko
dc.contributor.authorKing, John R.ko
dc.contributor.authorWinzer, Klausko
dc.contributor.authorTwycross, Jamieko
dc.contributor.authorMinton, Nigel P.ko
dc.date.accessioned2022-12-23T05:00:38Z-
dc.date.available2022-12-23T05:00:38Z-
dc.date.created2022-12-23-
dc.date.created2022-12-23-
dc.date.created2022-12-23-
dc.date.issued2022-05-
dc.identifier.citationPLOS COMPUTATIONAL BIOLOGY, v.18, no.5-
dc.identifier.issn1553-734X-
dc.identifier.urihttp://hdl.handle.net/10203/303634-
dc.description.abstractExploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. In this regard Cupriavidus necator H16 represents a particularly promising microbial chassis due to its ability to grow on a wide range of low-cost feedstocks, including the waste gas carbon dioxide, whilst also naturally producing large quantities of polyhydroxybutyrate (PHB) during nutrient-limited conditions. Understanding the complex metabolic behaviour of this bacterium is a prerequisite for the design of successful engineering strategies for optimising product yields. We present a genome-scale metabolic model (GSM) of C. necator H16 (denoted iCN1361), which is directly constructed from the BioCyc database to improve the readability and reusability of the model. After the initial automated construction, we have performed extensive curation and both theoretical and experimental validation. By carrying out a genome-wide essentiality screening using a Transposon-directed Insertion site Sequencing (TraDIS) approach, we showed that the model could predict gene knockout phenotypes with a high level of accuracy. Importantly, we indicate how experimental and computational predictions can be used to improve model structure and, thus, model Copyright: © 2022 Pearcy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.-
dc.languageEnglish-
dc.publisherPUBLIC LIBRARY SCIENCE-
dc.titleA genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications-
dc.typeArticle-
dc.identifier.wosid000944354300005-
dc.identifier.scopusid2-s2.0-85130843078-
dc.type.rimsART-
dc.citation.volume18-
dc.citation.issue5-
dc.citation.publicationnamePLOS COMPUTATIONAL BIOLOGY-
dc.identifier.doi10.1371/journal.pcbi.1010106-
dc.contributor.localauthorCho, Byung-Kwan-
dc.contributor.nonIdAuthorPearcy, Nicole-
dc.contributor.nonIdAuthorGaravaglia, Marco-
dc.contributor.nonIdAuthorMillat, Thomas-
dc.contributor.nonIdAuthorGilbert, James P.-
dc.contributor.nonIdAuthorHartman, Hassan-
dc.contributor.nonIdAuthorWoods, Craig-
dc.contributor.nonIdAuthorTomi-Andrino, Claudio-
dc.contributor.nonIdAuthorBommareddy, Rajesh Reddy-
dc.contributor.nonIdAuthorFell, David A.-
dc.contributor.nonIdAuthorPoolman, Mark-
dc.contributor.nonIdAuthorKing, John R.-
dc.contributor.nonIdAuthorWinzer, Klaus-
dc.contributor.nonIdAuthorTwycross, Jamie-
dc.contributor.nonIdAuthorMinton, Nigel P.-
dc.description.isOpenAccessN-
dc.type.journalArticleArticle-
dc.subject.keywordPlusPOLYHYDROXYBUTYRATE PRODUCTION-
dc.subject.keywordPlusESCHERICHIA-COLI-
dc.subject.keywordPlusGENE-
dc.subject.keywordPlusSTRATEGIES-
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