Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling
Abstract Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterize...
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| Format: | Article |
| Language: | English |
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Springer Nature
2013-04-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2013.6 |
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| author | Judith A H Wodke Jacek Puchałka Maria Lluch‐Senar Josep Marcos Eva Yus Miguel Godinho Ricardo Gutiérrez‐Gallego Vitor A P Martins dos Santos Luis Serrano Edda Klipp Tobias Maier |
| author_facet | Judith A H Wodke Jacek Puchałka Maria Lluch‐Senar Josep Marcos Eva Yus Miguel Godinho Ricardo Gutiérrez‐Gallego Vitor A P Martins dos Santos Luis Serrano Edda Klipp Tobias Maier |
| author_sort | Judith A H Wodke |
| collection | DOAJ |
| description | Abstract Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint‐based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time‐dependent changes, albeit using a static model. By performing an in silico knock‐out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms. |
| format | Article |
| id | doaj-art-c236d8f2c5a84d8ca86c47a1a6df1de4 |
| institution | DOAJ |
| issn | 1744-4292 |
| language | English |
| publishDate | 2013-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-c236d8f2c5a84d8ca86c47a1a6df1de42025-08-20T03:06:30ZengSpringer NatureMolecular Systems Biology1744-42922013-04-019111910.1038/msb.2013.6Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modelingJudith A H Wodke0Jacek Puchałka1Maria Lluch‐Senar2Josep Marcos3Eva Yus4Miguel Godinho5Ricardo Gutiérrez‐Gallego6Vitor A P Martins dos Santos7Luis Serrano8Edda Klipp9Tobias Maier10EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)Synthetic and Systems Biology Group, Helmholtz Center for Infection Research (HZI)EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)Department of Experimental and Health Sciences, Pompeu Fabra UniversityEMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)Synthetic and Systems Biology Group, Helmholtz Center for Infection Research (HZI)Department of Experimental and Health Sciences, Pompeu Fabra UniversitySynthetic and Systems Biology Group, Helmholtz Center for Infection Research (HZI)EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)Theoretical Biophysics, Humboldt‐Universität zu BerlinEMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)Abstract Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint‐based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time‐dependent changes, albeit using a static model. By performing an in silico knock‐out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms.https://doi.org/10.1038/msb.2013.6biomass compositionenergy metabolismin silico knock‐outsmetabolic modelingMycoplasma pneumonia |
| spellingShingle | Judith A H Wodke Jacek Puchałka Maria Lluch‐Senar Josep Marcos Eva Yus Miguel Godinho Ricardo Gutiérrez‐Gallego Vitor A P Martins dos Santos Luis Serrano Edda Klipp Tobias Maier Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling Molecular Systems Biology biomass composition energy metabolism in silico knock‐outs metabolic modeling Mycoplasma pneumonia |
| title | Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling |
| title_full | Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling |
| title_fullStr | Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling |
| title_full_unstemmed | Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling |
| title_short | Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling |
| title_sort | dissecting the energy metabolism in mycoplasma pneumoniae through genome scale metabolic modeling |
| topic | biomass composition energy metabolism in silico knock‐outs metabolic modeling Mycoplasma pneumonia |
| url | https://doi.org/10.1038/msb.2013.6 |
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