{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:55:59Z","timestamp":1787028959564,"version":"build-2736575974"},"reference-count":59,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T00:00:00Z","timestamp":1743206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003141","name":"SECIHTI and the Doctoral Program in Sciences in Biotechnological Processes at the University of Guadalajara","doi-asserted-by":"publisher","award":["1267568"],"award-info":[{"award-number":["1267568"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/metabo15040236","type":"journal-article","created":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T02:50:16Z","timestamp":1743389416000},"page":"236","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Influence of Amino Acids on Quorum Sensing-Related Pathways in Pseudomonas aeruginosa PAO1: Insights from the GEM iJD1249"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3856-4714","authenticated-orcid":false,"given":"Javier Alejandro","family":"Delgado-Nungaray","sequence":"first","affiliation":[{"name":"Chemical Engineering Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. Garc\u00eda Barrag\u00e1n # 1451, Guadalajara 44430, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7283-8035","authenticated-orcid":false,"given":"Luis Joel","family":"Figueroa-Y\u00e1\u00f1ez","sequence":"additional","affiliation":[{"name":"Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, A.C. (CIATEJ), Zapopan 45019, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8769-7407","authenticated-orcid":false,"given":"Eire","family":"Reynaga-Delgado","sequence":"additional","affiliation":[{"name":"Pharmacobiology Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. Garc\u00eda Barrag\u00e1n # 1451, Guadalajara 44430, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1947-9595","authenticated-orcid":false,"given":"Mario Alberto","family":"Garc\u00eda-Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Electronics Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. Garc\u00eda Barrag\u00e1n # 1451, Guadalajara 44430, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karla Esperanza","family":"Aguilar-Corona","sequence":"additional","affiliation":[{"name":"Food Engineering and Biotechnology, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. Garc\u00eda Barrag\u00e1n # 1451, Guadalajara 44430, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7721-1127","authenticated-orcid":false,"given":"Orfil","family":"Gonzalez-Reynoso","sequence":"additional","affiliation":[{"name":"Chemical Engineering Department, University Center for Exact and Engineering Sciences, University of Guadalajara, Blvd. M. Garc\u00eda Barrag\u00e1n # 1451, Guadalajara 44430, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,29]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2024). Bacterial Priority Pathogens List, 2024: Bacterial Pathogens of Public Health Importance to Guide Research, Development and Strategies to Prevent and Control Antimicrobial Resistance, WHO."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Thi, M.T.T., Wibowo, D., and Rehm, B.H.A. (2020). 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