iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6
A high-quality GSM model for Streptococcus pneumoniae R6 model strain (iDS372), comprising 372 genes and 529 reactions, was developed. The construction of this model involved performing a genome-wide reannotation to identify the metabolic capacity of the bacterium. A reaction representing the abstra...
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doaj-60ee9ec140fe40f683a113075cdc75a52020-11-25T02:44:11ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-06-011010.3389/fmicb.2019.01283457856iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6Oscar Dias0João Saraiva1Cristiana Faria2Mario Ramirez3Francisco Pinto4Isabel Rocha5Isabel Rocha6Centre of Biological Engineering, University of Minho, Braga, PortugalCentre of Biological Engineering, University of Minho, Braga, PortugalCentre of Biological Engineering, University of Minho, Braga, PortugalInstituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, PortugalBioISI – Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, PortugalCentre of Biological Engineering, University of Minho, Braga, PortugalInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, PortugalA high-quality GSM model for Streptococcus pneumoniae R6 model strain (iDS372), comprising 372 genes and 529 reactions, was developed. The construction of this model involved performing a genome-wide reannotation to identify the metabolic capacity of the bacterium. A reaction representing the abstraction of the biomass composition was reconciled from several studies reported in the literature and previous models, and included in the model. The final model comprises two compartments and manifold automatically generated gene rules. The validation was performed with experimental data from recent studies, regarding the usability of carbon sources, the effect of the presence of oxygen, and the requirement of amino acids for growth. This model can be used to better understand the metabolism of this major pathogen, provide clues regarding new drug targets, and eventually design strategies for fighting infections by these bacteria.https://www.frontiersin.org/article/10.3389/fmicb.2019.01283/fullgenome-scale metabolic modelStreptococcus pneumoniae R6metabolic reconstructioniDS372avirulentphenotypical reconciliation |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Oscar Dias João Saraiva Cristiana Faria Mario Ramirez Francisco Pinto Isabel Rocha Isabel Rocha |
spellingShingle |
Oscar Dias João Saraiva Cristiana Faria Mario Ramirez Francisco Pinto Isabel Rocha Isabel Rocha iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 Frontiers in Microbiology genome-scale metabolic model Streptococcus pneumoniae R6 metabolic reconstruction iDS372 avirulent phenotypical reconciliation |
author_facet |
Oscar Dias João Saraiva Cristiana Faria Mario Ramirez Francisco Pinto Isabel Rocha Isabel Rocha |
author_sort |
Oscar Dias |
title |
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 |
title_short |
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 |
title_full |
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 |
title_fullStr |
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 |
title_full_unstemmed |
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 |
title_sort |
ids372, a phenotypically reconciled model for the metabolism of streptococcus pneumoniae strain r6 |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2019-06-01 |
description |
A high-quality GSM model for Streptococcus pneumoniae R6 model strain (iDS372), comprising 372 genes and 529 reactions, was developed. The construction of this model involved performing a genome-wide reannotation to identify the metabolic capacity of the bacterium. A reaction representing the abstraction of the biomass composition was reconciled from several studies reported in the literature and previous models, and included in the model. The final model comprises two compartments and manifold automatically generated gene rules. The validation was performed with experimental data from recent studies, regarding the usability of carbon sources, the effect of the presence of oxygen, and the requirement of amino acids for growth. This model can be used to better understand the metabolism of this major pathogen, provide clues regarding new drug targets, and eventually design strategies for fighting infections by these bacteria. |
topic |
genome-scale metabolic model Streptococcus pneumoniae R6 metabolic reconstruction iDS372 avirulent phenotypical reconciliation |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2019.01283/full |
work_keys_str_mv |
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