Publication: Staphylococcus epidermidis RP62A’s Metabolic Network: Validation and Intervention Strategies
Authors
Guil Asensio, Francisco ; Sánchez-Cid, Guillermo ; García Carrasco, José Manuel
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Publisher
MDPI
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DOI
https://doi.org/10.3390/ metabo12090808
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info:eu-repo/semantics/article
Description
©2022. This manuscript version is made available under the CC-BY 4.0 license http://creativecommons.org/licenses/by /4.0/
This document is the Published, version of a Published Work that appeared in final form in Metabolites. To access the final edited and published work see https://doi.org/10.3390/ metabo12090808
Abstract
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 Staphylococcus epidermidis 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. S. epidermidis 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 Staphylococcus epidermidis 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
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Citation
Metabolites
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