<i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies
Increasingly, systems biology is gaining relevance in basic and applied research. The combination of computational biology with wet laboratory methods produces synergy that results in an exponential increase in knowledge of biological systems. The study of microorganisms such as <i>Staphylococ...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/12/9/808 |
| _version_ | 1797484907873697792 |
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| author | Francisco Guil Guillermo Sánchez-Cid José M. García |
| author_facet | Francisco Guil Guillermo Sánchez-Cid José M. García |
| author_sort | Francisco Guil |
| collection | DOAJ |
| description | Increasingly, systems biology is gaining relevance in basic and applied research. The combination of computational biology with wet laboratory methods produces synergy that results in an exponential increase in knowledge of biological systems. The study of microorganisms such as <i>Staphylococcus epidermidis</i> RP62A enables the researcher to understand better their metabolic networks, which allows the design of effective strategies to treat infections caused by this species or others. <i>S. epidermidis</i> is the second most commoncause of infection in patients with joint implants, so treating its proliferation seems vital for public health. There are different approaches to the analysis of metabolic networks. Flux balance analysis (FBA) is one of the most widespread streams of research. It allows the study of large metabolic networks, the study their structural properties, the optimization of metabolic flux, and the search for intervention strategies to modify the state of the metabolic network. This work presents the validation of the <i>Staphylococcus epidermidis</i> RP62A metabolic network model elaborated by Díaz Calvo et al. Then, we elaborate further on the network analysis’s essential reactions. The full set of essential reactions (including a previously unobserved one) was computed, and we classified them into equivalence classes. Some proposals to intervene in the network and design knock-outs by studying minimal cut sets of small length are also introduced. In particular, minimal cut sets related to the medium (including exchange reactions associated with medium metabolites) have been computed. In this sense, the unique external MCS (composed of cysteine and sulfate ion) has been found, and all hybrid MCS (based on knocking out both internal and exchange reactions) of length two have also been computed. The paper also points out the possible importance of these new intervention strategies. |
| first_indexed | 2024-03-09T23:12:09Z |
| format | Article |
| id | doaj.art-cce115f1ac764feabf48dad00803e98f |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-09T23:12:09Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-cce115f1ac764feabf48dad00803e98f2023-11-23T17:43:58ZengMDPI AGMetabolites2218-19892022-08-0112980810.3390/metabo12090808<i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention StrategiesFrancisco Guil0Guillermo Sánchez-Cid1José M. García2Grupo de Arquitectura y Computación Paralela, Universidad de Murcia, 30080 Murcia, SpainGrupo de Arquitectura y Computación Paralela, Universidad de Murcia, 30080 Murcia, SpainGrupo de Arquitectura y Computación Paralela, Universidad de Murcia, 30080 Murcia, SpainIncreasingly, systems biology is gaining relevance in basic and applied research. The combination of computational biology with wet laboratory methods produces synergy that results in an exponential increase in knowledge of biological systems. The study of microorganisms such as <i>Staphylococcus epidermidis</i> RP62A enables the researcher to understand better their metabolic networks, which allows the design of effective strategies to treat infections caused by this species or others. <i>S. epidermidis</i> is the second most commoncause of infection in patients with joint implants, so treating its proliferation seems vital for public health. There are different approaches to the analysis of metabolic networks. Flux balance analysis (FBA) is one of the most widespread streams of research. It allows the study of large metabolic networks, the study their structural properties, the optimization of metabolic flux, and the search for intervention strategies to modify the state of the metabolic network. This work presents the validation of the <i>Staphylococcus epidermidis</i> RP62A metabolic network model elaborated by Díaz Calvo et al. Then, we elaborate further on the network analysis’s essential reactions. The full set of essential reactions (including a previously unobserved one) was computed, and we classified them into equivalence classes. Some proposals to intervene in the network and design knock-outs by studying minimal cut sets of small length are also introduced. In particular, minimal cut sets related to the medium (including exchange reactions associated with medium metabolites) have been computed. In this sense, the unique external MCS (composed of cysteine and sulfate ion) has been found, and all hybrid MCS (based on knocking out both internal and exchange reactions) of length two have also been computed. The paper also points out the possible importance of these new intervention strategies.https://www.mdpi.com/2218-1989/12/9/808<i>Staphylococcus epidermidis</i>metabolic network validationminimal cut setsknock-outssystems biology |
| spellingShingle | Francisco Guil Guillermo Sánchez-Cid José M. García <i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies Metabolites <i>Staphylococcus epidermidis</i> metabolic network validation minimal cut sets knock-outs systems biology |
| title | <i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies |
| title_full | <i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies |
| title_fullStr | <i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies |
| title_full_unstemmed | <i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies |
| title_short | <i>Staphylococcus epidermidis</i> RP62A’s Metabolic Network: Validation and Intervention Strategies |
| title_sort | i staphylococcus epidermidis i rp62a s metabolic network validation and intervention strategies |
| topic | <i>Staphylococcus epidermidis</i> metabolic network validation minimal cut sets knock-outs systems biology |
| url | https://www.mdpi.com/2218-1989/12/9/808 |
| work_keys_str_mv | AT franciscoguil istaphylococcusepidermidisirp62asmetabolicnetworkvalidationandinterventionstrategies AT guillermosanchezcid istaphylococcusepidermidisirp62asmetabolicnetworkvalidationandinterventionstrategies AT josemgarcia istaphylococcusepidermidisirp62asmetabolicnetworkvalidationandinterventionstrategies |