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A key acid resistance mechanism of the facultative intracellular pathogen Salmonella is the expression of the arginine decarboxylase AdiA. While AdiA confers acid resistance via an H+-consuming reaction, we discover that the 3\u2032-untranslated region (UTR) of adiA mRNA is processed by RNase E into a regulatory small RNA, AdiZ. Through RNA\u2013RNA interactome profiling and transcriptomic analysis, followed by in vitro structural probing and in vivo validations, we demonstrate that AdiZ directly base-pairs with and negatively regulates ptsG, pykF, and dmsA mRNAs involved in glucose uptake, glycolysis, and anaerobic respiration, respectively. Intriguingly, AdiZ is induced and facilitates Salmonella survival within macrophages, where acidic and hypoxic stresses prevail. Thus, simultaneous expression of AdiA and AdiZ from a single mRNA ties arginine-dependent acid resistance to metabolic reprogramming of Salmonella in the host intracellular niches.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1371","type":"journal-article","created":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T13:15:10Z","timestamp":1763558110000},"source":"Crossref","is-referenced-by-count":5,"title":["3\u2032UTR-derived small RNA couples acid resistance to metabolic reprogramming of\n                    <i>Salmonella<\/i>\n                    within macrophages"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3587-5037","authenticated-orcid":false,"given":"Takeshi","family":"Kanda","sequence":"first","affiliation":[{"name":"Department of Infection Biology, Institute of Medicine, University of Tsukuba , 305-8575 Ibaraki ,","place":["Japan"]},{"name":"Transborder Medical Research Center, University of Tsukuba , 305-8575 Ibaraki 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University of Tsukuba , 305-8575 Ibaraki ,","place":["Japan"]},{"name":"Microbiology Research Center for Sustainability (MiCS), University of Tsukuba , 305-8572 Ibaraki ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3236-0169","authenticated-orcid":false,"given":"Alexander J","family":"Westermann","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080 W\u00fcrzburg ,","place":["Germany"]},{"name":"Department of Microbiology, Biocenter, University of W\u00fcrzburg , 97074 W\u00fcrzburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5735-7954","authenticated-orcid":false,"given":"Yanjie","family":"Chao","sequence":"additional","affiliation":[{"name":"Vaccine Research Center, Shanghai Institute of Materia Medica, University of Chinese Academy of 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