Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model
BACKGROUND: Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite develop...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6501404/ https://www.ncbi.nlm.nih.gov/pubmed/31060515 http://dx.doi.org/10.1186/s12859-019-2826-1 |
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author | Yan, Qiang Robert, Seth Brooks, J. Paul Fong, Stephen S. |
author_facet | Yan, Qiang Robert, Seth Brooks, J. Paul Fong, Stephen S. |
author_sort | Yan, Qiang |
collection | PubMed |
description | BACKGROUND: Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite development of bioprocessing applications. RESULTS: In this study, our goal was to characterize the metabolic profile of S. marcescens to provide insight for metabolic engineering applications and fundamental biological studies. Hereby, we constructed a constraint-based genome-scale metabolic model (iSR929) including 929 genes, 1185 reactions and 1164 metabolites based on genomic annotation of S. marcescens Db11. The model was tested by comparing model predictions with experimental data and analyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted). The model iSR929 was refined by integrating RNAseq data of S. marcescens growth on three different carbon sources (glucose, N-acetylglucosamine, and glycerol). Significant differences in TCA cycle utilization were found for growth on the different carbon substrates, For example, for growth on N-acetylglucosamine, S. marcescens exhibits high pentose phosphate pathway activity and nucleotide synthesis but low activity of the TCA cycle. CONCLUSIONS: Our results show that S. marcescens model iSR929 can provide reasonable predictions and can be constrained to fit with experimental values. Thus, our model may be used to guide strain designs for metabolic engineering to produce chemicals such as 2,3-butanediol, N-acetylneuraminic acid, and n-butanol using S. marcescens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2826-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6501404 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65014042019-05-10 Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model Yan, Qiang Robert, Seth Brooks, J. Paul Fong, Stephen S. BMC Bioinformatics Research Article BACKGROUND: Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite development of bioprocessing applications. RESULTS: In this study, our goal was to characterize the metabolic profile of S. marcescens to provide insight for metabolic engineering applications and fundamental biological studies. Hereby, we constructed a constraint-based genome-scale metabolic model (iSR929) including 929 genes, 1185 reactions and 1164 metabolites based on genomic annotation of S. marcescens Db11. The model was tested by comparing model predictions with experimental data and analyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted). The model iSR929 was refined by integrating RNAseq data of S. marcescens growth on three different carbon sources (glucose, N-acetylglucosamine, and glycerol). Significant differences in TCA cycle utilization were found for growth on the different carbon substrates, For example, for growth on N-acetylglucosamine, S. marcescens exhibits high pentose phosphate pathway activity and nucleotide synthesis but low activity of the TCA cycle. CONCLUSIONS: Our results show that S. marcescens model iSR929 can provide reasonable predictions and can be constrained to fit with experimental values. Thus, our model may be used to guide strain designs for metabolic engineering to produce chemicals such as 2,3-butanediol, N-acetylneuraminic acid, and n-butanol using S. marcescens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2826-1) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-06 /pmc/articles/PMC6501404/ /pubmed/31060515 http://dx.doi.org/10.1186/s12859-019-2826-1 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Yan, Qiang Robert, Seth Brooks, J. Paul Fong, Stephen S. Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model |
title | Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model |
title_full | Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model |
title_fullStr | Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model |
title_full_unstemmed | Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model |
title_short | Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model |
title_sort | metabolic characterization of the chitinolytic bacterium serratia marcescens using a genome-scale metabolic model |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6501404/ https://www.ncbi.nlm.nih.gov/pubmed/31060515 http://dx.doi.org/10.1186/s12859-019-2826-1 |
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