{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T12:47:05Z","timestamp":1787316425618,"version":"build-2736575974"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["ERC Consolidator Grant 865849-CAPSID"],"award-info":[{"award-number":["ERC Consolidator Grant 865849-CAPSID"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["doi.org\/10.55776\/COE7"],"award-info":[{"award-number":["doi.org\/10.55776\/COE7"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    is an opportunistic pathogen with high antibiotic resistance that infects immunocompromised patients. Its survival in diverse environments relies on nutrient uptake systems such as the dipeptide permease (Dpp), an ATP-binding cassette transporter that imports di- and tripeptides. Unlike other bacteria, whose Dpp includes a single solute-binding protein that binds substrates in the periplasm,\n                    <jats:italic>P. aeruginosa<\/jats:italic>\n                    encodes five paralogs (DppA1\u20135), the functional significance of which remains unclear. Here, we systematically profile the ligand specificities of all five DppA proteins using Differential Scanning Fluorimetry with a library of 281 di- and tripeptides. We find that DppA1 and DppA3 preferentially bind dipeptides, whereas DppA2 and DppA4 favor tripeptides. DppA5 shows no detectable binding, suggesting a divergent function. Ligand binding is highly structure-sensitive and distinct across DppA paralogs. A comparative reanalysis of published nutrient utilization data for\n                    <jats:italic>dppA1\u20135<\/jats:italic>\n                    suggests that previous studies underestimated this functional specialization. In contrast, our findings indicate that\n                    <jats:italic>P. aeruginosa<\/jats:italic>\n                    encodes multiple DppA paralogs to expand Dpp substrate scope and enhance nutrient acquisition. This work provides a foundation for further exploration of the Dpp in bacterial signaling and its exploitation for drug delivery via Trojan Horse antimicrobials.\n                  <\/jats:p>","DOI":"10.1038\/s41598-025-27865-2","type":"journal-article","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T12:21:57Z","timestamp":1766492517000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["The solute-binding proteins DppA1\u20135 of Pseudomonas aeruginosa have distinct substrate profiles"],"prefix":"10.1038","volume":"15","author":[{"given":"Konstantin","family":"Pl\u00f6chl","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"B\u00f6ttcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,23]]},"reference":[{"key":"27865_CR1","doi-asserted-by":"publisher","first-page":"2221","DOI":"10.1016\/s0140-6736(22)02185-7","volume":"400","author":"KS Ikuta","year":"2022","unstructured":"Ikuta, K. S. et al. Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet 400, 2221\u20132248. https:\/\/doi.org\/10.1016\/s0140-6736(22)02185-7 (2022).","journal-title":"Lancet"},{"key":"27865_CR2","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1099\/mic.0.000860","volume":"166","author":"SP Diggle","year":"2020","unstructured":"Diggle, S. P., Whiteley, M. Microbe Profile:\u00a0Pseudomonas aeruginosa: opportunistic pathogen and lab rat. Microbiol. (Reading). 166, 30\u201333. https:\/\/doi.org\/10.1099\/mic.0.000860 (2020).","journal-title":"Microbiol. (Reading)"},{"key":"27865_CR3","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1586\/eri.13.12","volume":"11","author":"JN Pendleton","year":"2013","unstructured":"Pendleton, J. N., Gorman, S. P. & Gilmore, B. F. Clinical relevance of the ESKAPE pathogens. Expert Rev. Anti Infect. Ther. 11, 297\u2013308. https:\/\/doi.org\/10.1586\/eri.13.12 (2013).","journal-title":"Expert Rev. Anti Infect. Ther."},{"key":"27865_CR4","unstructured":"World Health Organization. Prioritization of pathogens to guide discovery, research and development of new antibiotics for drug-resistant bacterial infections, including tuberculosis. Geneva. (2017)."},{"key":"27865_CR5","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/35023079","volume":"406","author":"CK Stover","year":"2000","unstructured":"Stover, C. K. et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406, 959\u2013964. https:\/\/doi.org\/10.1038\/35023079 (2000).","journal-title":"Nature"},{"key":"27865_CR6","doi-asserted-by":"publisher","first-page":"2209","DOI":"10.1099\/mic.0.2007\/015032-0","volume":"154","author":"PD Kiely","year":"2008","unstructured":"Kiely, P. D., O\u2019Callaghan, J., Abbas, A. & O\u2019Gara, F. Genetic analysis of genes involved in dipeptide metabolism and cytotoxicity in Pseudomonas aeruginosa PAO1. Microbiol. (Reading). 154, 2209\u20132218. https:\/\/doi.org\/10.1099\/mic.0.2007\/015032-0 (2008).","journal-title":"Microbiol. (Reading)"},{"key":"27865_CR7","doi-asserted-by":"publisher","first-page":"e111311","DOI":"10.1371\/journal.pone.0111311","volume":"9","author":"D Pletzer","year":"2014","unstructured":"Pletzer, D. et al. High-throughput screening of dipeptide utilization mediated by the ABC transporter DppBCDF and its substrate-binding proteins DppA1-A5 in Pseudomonas aeruginosa. PLoS One. 9, e111311. https:\/\/doi.org\/10.1371\/journal.pone.0111311 (2014).","journal-title":"PLoS One"},{"key":"27865_CR8","doi-asserted-by":"publisher","first-page":"2217","DOI":"10.1128\/JB.00234-15","volume":"197","author":"D Pletzer","year":"2015","unstructured":"Pletzer, D. et al. The Pseudomonas aeruginosa PA14 ABC transporter NppA1A2BCD is required for uptake of peptidyl nucleoside antibiotics. J. Bacteriol. 197, 2217\u20132228. https:\/\/doi.org\/10.1128\/JB.00234-15 (2015).","journal-title":"J. Bacteriol."},{"key":"27865_CR9","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1007\/s10482-016-0675-8","volume":"109","author":"D Pletzer","year":"2016","unstructured":"Pletzer, D., Braun, Y. & Weingart, H. Swarming motility is modulated by expression of the putative xenosiderophore transporter SppR-SppABCD in Pseudomonas aeruginosa PA14. Antonie Van Leeuwenhoek. 109, 737\u2013753. https:\/\/doi.org\/10.1007\/s10482-016-0675-8 (2016).","journal-title":"Antonie Van Leeuwenhoek"},{"key":"27865_CR10","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1128\/JB.188.1.45-54.2006","volume":"188","author":"S Tamber","year":"2006","unstructured":"Tamber, S., Ochs, M. M. & Hancock, R. E. Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa. J. Bacteriol. 188, 45\u201354. https:\/\/doi.org\/10.1128\/JB.188.1.45-54.2006 (2006).","journal-title":"J. Bacteriol."},{"key":"27865_CR11","unstructured":"McGowan, D. Characterization of the Chp System of Pseudomonas aeruginosa. PhD thesis, Monash University. https:\/\/doi.org\/10.4225\/03\/58b8a8993e670 (2016)."},{"key":"27865_CR12","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00030","author":"Y Lee","year":"2018","unstructured":"Lee, Y. et al. Substrate binding protein DppA1 of ABC transporter DppBCDF increases biofilm formation in Pseudomonas aeruginosa by inhibiting Pf5 prophage lysis. Front. Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2018.00030 (2018).","journal-title":"Front. Microbiol."},{"key":"27865_CR13","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1128\/jb.173.1.234-244.1991","volume":"173","author":"ER Olson","year":"1991","unstructured":"Olson, E. R., Dunyak, D. S., Jurss, L. M. & Poorman, R. A. Identification and characterization of dppA, an Escherichia coli gene encoding a periplasmic dipeptide transport protein. J. Bacteriol. 173, 234\u2013244. https:\/\/doi.org\/10.1128\/jb.173.1.234-244.1991 (1991).","journal-title":"J. Bacteriol."},{"key":"27865_CR14","doi-asserted-by":"publisher","first-page":"633166","DOI":"10.3389\/fmicb.2021.633166","volume":"12","author":"X Xu","year":"2021","unstructured":"Xu, X. et al. The role of a dipeptide transporter in the virulence of human pathogen, Helicobacter pylori. Front. Microbiol. 12, 633166. https:\/\/doi.org\/10.3389\/fmicb.2021.633166 (2021).","journal-title":"Front. Microbiol."},{"key":"27865_CR15","doi-asserted-by":"publisher","first-page":"5156","DOI":"10.3390\/ijms20205156","volume":"20","author":"M Fernandez","year":"2019","unstructured":"Fernandez, M. et al. Determination of ligand profiles for Pseudomonas aeruginosa solute binding proteins. Int. J. Mol. 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ColabFold: making protein folding accessible to all. Nat. Methods. 19, 679\u2013682. https:\/\/doi.org\/10.1038\/s41592-022-01488-1 (2022).","journal-title":"Nat. Methods"},{"key":"27865_CR19","doi-asserted-by":"publisher","first-page":"e0205422","DOI":"10.1128\/spectrum.02054-22","volume":"10","author":"A Ortega","year":"2022","unstructured":"Ortega, A., Matilla, M. A. & Krell, T. The repertoire of solute-binding proteins of model bacteria reveals large differences in number, type, and ligand range. Microbiol. Spectr. 10, e0205422. https:\/\/doi.org\/10.1128\/spectrum.02054-22 (2022).","journal-title":"Microbiol. Spectr."},{"key":"27865_CR20","doi-asserted-by":"publisher","first-page":"2327","DOI":"10.1002\/pro.5560041110","volume":"4","author":"P Dunten","year":"1995","unstructured":"Dunten, P. & Mowbray, S. L. Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis. Protein Sci. 4, 2327\u20132334. https:\/\/doi.org\/10.1002\/pro.5560041110 (1995).","journal-title":"Protein Sci."},{"key":"27865_CR21","doi-asserted-by":"publisher","first-page":"4393","DOI":"10.1002\/1873-3468.12445","volume":"590","author":"GH Scheepers","year":"2016","unstructured":"Scheepers, G. H., Lycklama, A., Nijeholt, J. A. & Poolman, B. An updated structural classification of substrate-binding proteins. FEBS Lett. 590, 4393\u20134401. https:\/\/doi.org\/10.1002\/1873-3468.12445 (2016).","journal-title":"FEBS Lett."},{"key":"27865_CR22","doi-asserted-by":"publisher","first-page":"2606","DOI":"10.1016\/j.febslet.2010.04.043","volume":"584","author":"RPA Berntsson","year":"2010","unstructured":"Berntsson, R. P. A., Smits, S. H. J., Schmitt, L., Slotboom, D. J. & Poolman, B. A structural classification of substrate-binding proteins. 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Science https:\/\/doi.org\/10.1126\/science.aat9691 (2019).","journal-title":"Science"},{"key":"27865_CR25","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1038\/s41570-021-00313-1","volume":"5","author":"M Miethke","year":"2021","unstructured":"Miethke, M. et al. Towards the sustainable discovery and development of new antibiotics. Nat. Rev. Chem. 5, 726\u2013749. https:\/\/doi.org\/10.1038\/s41570-021-00313-1 (2021).","journal-title":"Nat. Rev. Chem."},{"key":"27865_CR26","doi-asserted-by":"publisher","first-page":"5565","DOI":"10.1128\/AAC.01198-13","volume":"57","author":"A Mistry","year":"2013","unstructured":"Mistry, A. et al. High-level pacidamycin resistance in Pseudomonas aeruginosa is mediated by an Opp oligopeptide permease encoded by the opp-fabI\u00a0operon. Antimicrob. Agents Chemother. 57, 5565\u20135571. https:\/\/doi.org\/10.1128\/AAC.01198-13 (2013).","journal-title":"Antimicrob. 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Protein Sci. 16, 30\u201342. https:\/\/doi.org\/10.1110\/ps.062558507 (2007).","journal-title":"Protein Sci."},{"key":"27865_CR29","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1038\/nsb1096-842","volume":"3","author":"WC Wimley","year":"1996","unstructured":"Wimley, W. C. & White, S. H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3, 842\u2013848. https:\/\/doi.org\/10.1038\/nsb1096-842 (1996).","journal-title":"Nat. Struct. Biol."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-27865-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-27865-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-27865-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T01:02:48Z","timestamp":1766538168000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-27865-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,23]]},"references-count":29,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["27865"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-27865-2","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,23]]},"assertion":[{"value":"14 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"44346"}}