{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T22:03:31Z","timestamp":1791842611584,"version":"4.3.4"},"update-to":[{"DOI":"10.1371\/journal.ppat.1009280","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T00:00:00Z","timestamp":1631232000000}}],"reference-count":152,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2021,8,30]],"date-time":"2021-08-30T00:00:00Z","timestamp":1630281600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["106914\/Z\/15\/Z"],"award-info":[{"award-number":["106914\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI007025"],"award-info":[{"award-number":["AI007025"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Paul G. Allen School for Global Animal Health"},{"name":"College of Veterinary Medicine, Washington State University"},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    serovar Typhimurium (\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis,\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium colonizes epithelial cells lining the gastrointestinal tract.\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived\n                    <jats:italic>Salmonella<\/jats:italic>\n                    -containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium within the epithelial cytosol, and the bacterial genes required for cytosolic colonization, remain largely unknown. Here we have exploited the parallel colonization strategies of\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes with cytosol-induced or vacuole-induced expression signatures. Using these genes as environmental biosensors, we defined that\n                    <jats:italic>Salmonella<\/jats:italic>\n                    is exposed to oxidative stress and iron and manganese deprivation in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium replication in the cytosol, as well as\n                    <jats:italic>entC<\/jats:italic>\n                    ,\n                    <jats:italic>fepB<\/jats:italic>\n                    ,\n                    <jats:italic>soxS<\/jats:italic>\n                    ,\n                    <jats:italic>mntH<\/jats:italic>\n                    and\n                    <jats:italic>sitA<\/jats:italic>\n                    . Virulence genes that are typically associated with extracellular bacteria, namely\n                    <jats:italic>Salmonella<\/jats:italic>\n                    pathogenicity island 1 (SPI1) and SPI4, showed increased expression in the cytosol compared to vacuole. Our study reveals that the cytosolic and vacuolar\n                    <jats:italic>S<\/jats:italic>\n                    . Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. This archetypical vacuole-adapted pathogen therefore requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1009280","type":"journal-article","created":{"date-parts":[[2021,8,30]],"date-time":"2021-08-30T13:33:15Z","timestamp":1630330395000},"page":"e1009280","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":66,"title":["Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0762-6316","authenticated-orcid":true,"given":"TuShun R.","family":"Powers","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda L.","family":"Haeberle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2750-1599","authenticated-orcid":true,"given":"Alexander V.","family":"Predeus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8077-7615","authenticated-orcid":true,"given":"Disa L.","family":"Hammarl\u00f6f","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3955-8226","authenticated-orcid":true,"given":"Jennifer A.","family":"Cundiff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeus","family":"Salda\u00f1a-Ahuactzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7464-2370","authenticated-orcid":true,"given":"Karsten","family":"Hokamp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2671-6026","authenticated-orcid":true,"given":"Jay C. D.","family":"Hinton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3028-2198","authenticated-orcid":true,"given":"Leigh A.","family":"Knodler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,8,30]]},"reference":[{"key":"ppat.1009280.ref001","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.tim.2014.01.003","article-title":"Cytoplasmic access by intracellular bacterial pathogens","volume":"22","author":"J Fredlund","year":"2014","journal-title":"Trends in Microbiology"},{"key":"ppat.1009280.ref002","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.mib.2014.10.010","article-title":"Salmonella enterica: living a double life in epithelial cells","volume":"23","author":"LA Knodler","year":"2015","journal-title":"Current Opinion in Microbiology"},{"key":"ppat.1009280.ref003","doi-asserted-by":"crossref","first-page":"136","DOI":"10.3389\/fcimb.2018.00136","article-title":"To Be Cytosolic or Vacuolar: The Double Life of Listeria monocytogenes","volume":"8","author":"H Bierne","year":"2018","journal-title":"Front Cell Infect Microbiol"},{"key":"ppat.1009280.ref004","doi-asserted-by":"crossref","first-page":"e1001921","DOI":"10.1371\/journal.pmed.1001921","article-title":"World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis.","volume":"12","author":"MD Kirk","year":"2015","journal-title":"PLOS Medicine."},{"key":"ppat.1009280.ref005","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1016\/S1473-3099(19)30418-9","article-title":"The global burden of non-typhoidal Salmonella invasive disease: a systematic analysis for the Global Burden of Disease Study 2017","volume":"19","author":"JD Stanaway","year":"2019","journal-title":"The Lancet Infectious Diseases"},{"key":"ppat.1009280.ref006","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1046\/j.1462-5822.1999.00003.x","article-title":"Biogenesis of Salmonella typhimurium-containing vacuoles in epithelial cells involves interactions with the early endocytic pathway","volume":"1","author":"O Steele-Mortimer","year":"1999","journal-title":"Cellular Microbiology"},{"key":"ppat.1009280.ref007","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1111\/j.1600-0854.2006.00529.x","article-title":"Salmonella trafficking is defined by continuous dynamic interactions with the endolysosomal system","volume":"8","author":"D Drecktrah","year":"2007","journal-title":"Traffic"},{"key":"ppat.1009280.ref008","doi-asserted-by":"crossref","first-page":"348","DOI":"10.3389\/fcimb.2017.00348","article-title":"Swiss Army Pathogen: The Salmonella Entry Toolkit.","volume":"7","author":"PJ Hume","year":"2017","journal-title":"Front Cell Infect Microbiol"},{"key":"ppat.1009280.ref009","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1046\/j.1365-2958.1999.01312.x","article-title":"Environmental regulation of Salmonella pathogenicity island 2 gene expression","volume":"31","author":"J Deiwick","year":"1999","journal-title":"Mol Microbiol"},{"key":"ppat.1009280.ref010","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1046\/j.1365-2958.1999.01527.x","article-title":"pH-dependent secretion of SseB, a product of the SPI-2 type III secretion system of Salmonella typhimurium","volume":"33","author":"CR Beuz\u00f3n","year":"1999","journal-title":"Molecular Microbiology"},{"key":"ppat.1009280.ref011","doi-asserted-by":"crossref","first-page":"432","DOI":"10.3389\/fcimb.2017.00432","article-title":"Salmonella Populations inside Host Cells","volume":"7","author":"S Castanheira","year":"2017","journal-title":"Front Cell Infect Microbiol"},{"key":"ppat.1009280.ref012","doi-asserted-by":"crossref","first-page":"17733","DOI":"10.1073\/pnas.1006098107","article-title":"Dissemination of invasive Salmonella via bacterial-induced extrusion of mucosal epithelia","volume":"107","author":"LA Knodler","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"ppat.1009280.ref013","doi-asserted-by":"crossref","first-page":"e38732","DOI":"10.1371\/journal.pone.0038732","article-title":"The bimodal lifestyle of intracellular Salmonella in epithelial cells: replication in the cytosol obscures defects in vacuolar replication.","volume":"7","author":"P Malik-Kale","year":"2012","journal-title":"PLoS ONE"},{"key":"ppat.1009280.ref014","doi-asserted-by":"crossref","first-page":"e84681","DOI":"10.1371\/journal.pone.0084681","article-title":"Quantitative assessment of cytosolic Salmonella in epithelial cells.","volume":"9","author":"LA Knodler","year":"2014","journal-title":"PLoS ONE"},{"key":"ppat.1009280.ref015","first-page":"65","article-title":"Decoding a Salmonella Typhi Regulatory Network that Controls Typhoid Toxin Expression within Human Cells. 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