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A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network

A minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential...

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Autores principales: Ye, Yuan-Nong, Ma, Bin-Guang, Dong, Chuan, Zhang, Hong, Chen, Ling-Ling, Guo, Feng-Biao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054358/
https://www.ncbi.nlm.nih.gov/pubmed/27713529
http://dx.doi.org/10.1038/srep35082
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author Ye, Yuan-Nong
Ma, Bin-Guang
Dong, Chuan
Zhang, Hong
Chen, Ling-Ling
Guo, Feng-Biao
author_facet Ye, Yuan-Nong
Ma, Bin-Guang
Dong, Chuan
Zhang, Hong
Chen, Ling-Ling
Guo, Feng-Biao
author_sort Ye, Yuan-Nong
collection PubMed
description A minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. Second, we introduced a half-retaining strategy to extract persistent essential genes to ensure stability. Third, we constructed a viable metabolic network to supplement SBGS. The proposed SBGS includes 327 genes and required 431 reactions. This report describes an SBGS that preserves both self-replication and self-maintenance systems. In the minimized metabolic network, we identified five novel hub metabolites and confirmed 20 known hubs. Highly essential genes were found to distribute the connecting metabolites into more reactions. Based on our SBGS, we expanded the pool of targets for designing broad-spectrum antibacterial drugs to reduce pathogen resistance. We also suggested a rough semi-de novo strategy to synthesize an artificial cell, with potential applications in industry.
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spelling pubmed-50543582016-10-19 A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network Ye, Yuan-Nong Ma, Bin-Guang Dong, Chuan Zhang, Hong Chen, Ling-Ling Guo, Feng-Biao Sci Rep Article A minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. Second, we introduced a half-retaining strategy to extract persistent essential genes to ensure stability. Third, we constructed a viable metabolic network to supplement SBGS. The proposed SBGS includes 327 genes and required 431 reactions. This report describes an SBGS that preserves both self-replication and self-maintenance systems. In the minimized metabolic network, we identified five novel hub metabolites and confirmed 20 known hubs. Highly essential genes were found to distribute the connecting metabolites into more reactions. Based on our SBGS, we expanded the pool of targets for designing broad-spectrum antibacterial drugs to reduce pathogen resistance. We also suggested a rough semi-de novo strategy to synthesize an artificial cell, with potential applications in industry. Nature Publishing Group 2016-10-07 /pmc/articles/PMC5054358/ /pubmed/27713529 http://dx.doi.org/10.1038/srep35082 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Ye, Yuan-Nong
Ma, Bin-Guang
Dong, Chuan
Zhang, Hong
Chen, Ling-Ling
Guo, Feng-Biao
A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
title A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
title_full A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
title_fullStr A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
title_full_unstemmed A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
title_short A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
title_sort novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054358/
https://www.ncbi.nlm.nih.gov/pubmed/27713529
http://dx.doi.org/10.1038/srep35082
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