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...

Descripción completa

Detalles Bibliográficos
Autores principales: Yan, Qiang, Robert, Seth, Brooks, J. Paul, Fong, Stephen S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
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
_version_ 1783416107447615488
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
work_keys_str_mv AT yanqiang metaboliccharacterizationofthechitinolyticbacteriumserratiamarcescensusingagenomescalemetabolicmodel
AT robertseth metaboliccharacterizationofthechitinolyticbacteriumserratiamarcescensusingagenomescalemetabolicmodel
AT brooksjpaul metaboliccharacterizationofthechitinolyticbacteriumserratiamarcescensusingagenomescalemetabolicmodel
AT fongstephens metaboliccharacterizationofthechitinolyticbacteriumserratiamarcescensusingagenomescalemetabolicmodel