BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL2504040001?filename=iJD1249.xlsxprimaryOK200Javier Alejandro Delgado NungarayNon-curatedsteady-state model*https://www.ebi.ac.uk/biomodels/MODEL2504040001falseBioModelsOtherModelsiJD1249 Pseudomonas aeruginosa PAO1MODEL2504040001Javier Alejandro Delgado Nungaray, Orfil Gonzalez-ReynosoJavier Alejandro Delgado Nungaray10.3390/metabo15040236, first_pagesettingsOrder Article Reprints Open AccessArticle Influence of Amino Acids on Quorum Sensing-Related Pathways in Pseudomonas aeruginosa PAO1: Insights from the GEM iJD1249 by Javier Alejandro Delgado-Nungaray 1ORCID,Luis Joel Figueroa-Yáñez 2ORCID,Eire Reynaga-Delgado 3ORCID,Mario Alberto García-Ramírez 4ORCID,Karla Esperanza Aguilar-Corona 5 andOrfil Gonzalez-Reynoso 1,*ORCID 1 Chemical Engineering Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. García Barragán # 1451, Guadalajara 44430, Mexico 2 Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, A.C. (CIATEJ), Zapopan 45019, Mexico 3 Pharmacobiology Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. García Barragán # 1451, Guadalajara 44430, Mexico 4 Electronics Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. García Barragán # 1451, Guadalajara 44430, Mexico 5 Food Engineering and Biotechnology, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. García Barragán # 1451, Guadalajara 44430, Mexico * Author to whom correspondence should be addressed. Metabolites 2025, 15(4), 236; https://doi.org/10.3390/metabo15040236 Submission received: 7 March 2025 / Revised: 20 March 2025 / Accepted: 26 March 2025 / Published: 29 March 2025 (This article belongs to the Special Issue Biostatistics and Bioinformatics in Metabolomics Research: From Study Design and Analytics to Clinical Insights and Public Health Implications) Downloadkeyboard_arrow_down Browse Figures Review Reports Versions Notes Abstract Background/objectives: Amino acids (AAs) play a critical role in diseases such as cystic fibrosis where Pseudomonas aeruginosa PAO1 adapts its metabolism in response to host-derived nutrients. The adaptation influences virulence and complicates antibiotic treatment mainly for the antimicrobial resistance context. D- and L-AAs have been analyzed for their impact on quorum sensing (QS), a mechanism that regulates virulence factors. This research aimed to reconstruct the genome-scale metabolic model (GEM) of P. aeruginosa PAO1 to investigate the metabolic roles of D- and L-AAs in QS-related pathways. Methods: The updated GEM, iJD1249, was reconstructed by using protocols to integrate data from previous models and refined with well-standardized in silico media (LB, M9, and SCFM) to improve flux balance analysis accuracy. The model was used to explore the metabolic impact of D-Met, D-Ala, D-Glu, D-Ser, L-His, L-Glu, L-Arg, and L-Ornithine (L-Orn) at 5 and 50 mM in QS-related pathways, focusing on the effects on bacterial growth and carbon flux distributions. Results: Among the tested AAs, D-Met was the only one that did not enhance the growth rate of P. aeruginosa PAO1, while L-Arg and L-Orn increased fluxes in the L-methionine biosynthesis pathway, influencing the metH gene. These findings suggest a differential metabolic role for D-and L-AAs in QS-related pathways. Conclusions: Our results shed some light on the metabolic impact of AAs on QS-related pathways and their potential role in P. aeruginosa virulence. Future studies should assess D-Met as a potential adjuvant in antimicrobial strategies, optimizing the concentration in combination with antibiotics to maximize its therapeutic effectiveness. null, null. Universidad de Guadalajarajavier.dnungaray@gmail.com10.3390/metabo15040236Universidad de GuadalajarafalseiJD1249 - Pseudomonas aeruginosa PAO1No description2025-04-042025-04-072025-04-04MODEL2504040001MODEL250404000110.3390/metabo15040236