{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:57:24Z","timestamp":1782280644428,"version":"3.54.5"},"posted":{"date-parts":[[2025,12,30]]},"group-title":"Microbiology","reference-count":77,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T00:00:00Z","timestamp":1767052800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["140167"],"award-info":[{"award-number":["140167"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["AI154305"],"award-info":[{"award-number":["AI154305"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["AI182210"],"award-info":[{"award-number":["AI182210"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,12,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  <jats:italic>Chlamydia trachomatis<\/jats:italic>\n                  is a leading cause of urogenital infections that can result in serious long-term complications. This obligate intracellular bacterium undergoes a biphasic developmental cycle alternating between the infectious elementary body and the replicative reticulate body and can enter a persistent state in response to adverse environmental conditions. Although transcriptomic reprogramming is central to chlamydial stress adaptation and persistence, how responses differ across biologically distinct stressors remains incompletely defined. Here, we performed a comparative reanalysis of five published, high-quality\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  RNA-Seq datasets generated under prolonged interferon-\u03b3 treatment, tryptophan starvation, iron starvation, penicillin exposure, or acute heat shock. Global transcriptomic analyses reveal extensive stress-specific reprogramming and a clear separation between the transcriptome induced by heat shock and those induced by chronic stresses. Transcriptomic overlap observed among chronic stress conditions is substantially reduced when the heat shock transcriptome is included, indicating that shared transcriptional features are stressor-dependent. Unexpectedly, tryptophan starvation and iron starvation exhibit particularly close transcriptomic similarity, consistent with regulatory cross-talk mediated by the iron-dependent transcriptional repressor YtgR. In contrast, interferon-\u03b3 induces a distinct but partially overlapping transcriptome, likely reflecting activation of additional host-mediated antimicrobial mechanisms beyond tryptophan deprivation. Together, these findings demonstrate that adaptation to different biological stressors in\n                  <jats:italic>C. trachomatis<\/jats:italic>\n                  is driven by distinct transcriptomic reprogramming, while consistently involving a subset of functions that may represent points of vulnerability for disrupting chlamydial persistence.\n                <\/jats:p>","DOI":"10.64898\/2025.12.30.696969","type":"posted-content","created":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T13:10:15Z","timestamp":1767100215000},"source":"Crossref","is-referenced-by-count":0,"title":["Comparative Transcriptomics Reveals Genes Commonly Induced by Distinct Stressors in\n                  <i>Chlamydia<\/i>"],"prefix":"10.64898","author":[{"given":"Ronald","family":"Haines","sequence":"first","affiliation":[{"name":"Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8262-8173","authenticated-orcid":false,"given":"Danny","family":"Wan","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7053-5009","authenticated-orcid":false,"given":"Guangming","family":"Zhong","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Texas Health San Antonio, San Antonio, TX 78229, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4903-926X","authenticated-orcid":false,"given":"Huizhou","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026010207150645000_2025.12.30.696969v1.1","doi-asserted-by":"crossref","unstructured":"Harms A , Maisonneuve E , Gerdes K . 2016. 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