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MCF2Chem: A manually curated knowledge base of biosynthetic compound production

BACKGROUND: Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these...

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Autores principales: Cai, Pengli, Liu, Sheng, Zhang, Dachuan, Hu, Qian-Nan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10625697/
https://www.ncbi.nlm.nih.gov/pubmed/37925500
http://dx.doi.org/10.1186/s13068-023-02419-8
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author Cai, Pengli
Liu, Sheng
Zhang, Dachuan
Hu, Qian-Nan
author_facet Cai, Pengli
Liu, Sheng
Zhang, Dachuan
Hu, Qian-Nan
author_sort Cai, Pengli
collection PubMed
description BACKGROUND: Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds. RESULTS: In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that “fatty acids”, “terpenoids”, and “shikimates and phenylpropanoids” accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities. CONCLUSIONS: MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com. This database may serve as a useful resource for synthetic biologists. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-023-02419-8.
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spelling pubmed-106256972023-11-06 MCF2Chem: A manually curated knowledge base of biosynthetic compound production Cai, Pengli Liu, Sheng Zhang, Dachuan Hu, Qian-Nan Biotechnol Biofuels Bioprod Methodology BACKGROUND: Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds. RESULTS: In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that “fatty acids”, “terpenoids”, and “shikimates and phenylpropanoids” accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities. CONCLUSIONS: MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com. This database may serve as a useful resource for synthetic biologists. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-023-02419-8. BioMed Central 2023-11-04 /pmc/articles/PMC10625697/ /pubmed/37925500 http://dx.doi.org/10.1186/s13068-023-02419-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Methodology
Cai, Pengli
Liu, Sheng
Zhang, Dachuan
Hu, Qian-Nan
MCF2Chem: A manually curated knowledge base of biosynthetic compound production
title MCF2Chem: A manually curated knowledge base of biosynthetic compound production
title_full MCF2Chem: A manually curated knowledge base of biosynthetic compound production
title_fullStr MCF2Chem: A manually curated knowledge base of biosynthetic compound production
title_full_unstemmed MCF2Chem: A manually curated knowledge base of biosynthetic compound production
title_short MCF2Chem: A manually curated knowledge base of biosynthetic compound production
title_sort mcf2chem: a manually curated knowledge base of biosynthetic compound production
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10625697/
https://www.ncbi.nlm.nih.gov/pubmed/37925500
http://dx.doi.org/10.1186/s13068-023-02419-8
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