{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T21:09:16Z","timestamp":1780607356939,"version":"3.54.1"},"reference-count":20,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T00:00:00Z","timestamp":1739491200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Nonexpressor of pathogenesis-related 1 (NPR1) is crucial for activating the plant immune system through the signaling molecule salicylic acid (SA), which triggers systemic acquired resistance (SAR) in <jats:italic>Arabidopsis<\/jats:italic>. In this study, three putative genes associated with NPR1 from <jats:italic>Arabidopsis<\/jats:italic> have been identified in the genome of <jats:italic>Theobroma cacao<\/jats:italic>, namely, <jats:italic>TcNPR1, TcNPR2<\/jats:italic>, and <jats:italic>TcNPR3<\/jats:italic>, suggesting a functional diversification among the three gene entities. Phylogenetic analysis revealed that <jats:italic>TcNPR1<\/jats:italic> and <jats:italic>TcNPR2<\/jats:italic> branched alongside their Arabidopsis orthologs, <jats:italic>NPR1<\/jats:italic> and <jats:italic>NPR2<\/jats:italic>, indicating that these genes maintain a conserved role in SA signaling pathways across different species. In contrast, <jats:italic>TcNPR3<\/jats:italic> exists in a separate clade, suggesting unique functional roles and evolutionary divergence. A comparative analysis of the physiochemical properties of these <jats:italic>TcNPRs<\/jats:italic> showed a different subcellular localization, as <jats:italic>TcNPR1<\/jats:italic> persists in the cytoplasm, while <jats:italic>TcNPR3<\/jats:italic> is found in the nucleus, aligning with its proposed role in SA signaling and transcriptional regulation. Furthermore, we identified microRNAs that target <jats:italic>TcNPR3,<\/jats:italic> suggesting that <jats:italic>P. megakarya<\/jats:italic> may exploit the transcriptional regulatory network to bypass plant defense activation. Transient overexpression or suppression of <jats:italic>TcNPR<\/jats:italic> gene expression through RNA interference-mediated gene silencing could be sufficient to study the impact on the production of other molecules, such as SA, some PR protein expressions, and resistance against <jats:italic>P. megakarya<\/jats:italic>. The interactions between proteins encoded by <jats:italic>TcNPRs<\/jats:italic> and cellular proteins of <jats:italic>P. megakarya<\/jats:italic> will provide insight into whether the pathogen manipulates host defenses. Finally, the expression of <jats:italic>TcNPR<\/jats:italic> genes in response to infection by <jats:italic>P. megakarya<\/jats:italic> offers valuable information regarding the temporal and spatial activation during the defense response.<\/jats:p>","DOI":"10.1371\/journal.pone.0318506","type":"journal-article","created":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T18:35:27Z","timestamp":1739558127000},"page":"e0318506","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["NPR1-like genes in Theobroma cacao: Evolutionary insights and potential in enhancing resistance to Phytophthora megakarya"],"prefix":"10.1371","volume":"20","author":[{"given":"Muhammad Umar","family":"Rasheed","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiman","family":"Malik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Zeshan","family":"Haider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adnan","family":"Sami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Shafiq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qurban","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Arshad","family":"Javed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4113-6137","authenticated-orcid":true,"given":"Ansar","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,2,14]]},"reference":[{"issue":"4","key":"pone.0318506.ref001","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.pbi.2004.05.006","article-title":"NPR1: the spider in the web of induced resistance signaling pathways","volume":"7","author":"CMJ Pieterse","year":"2004","journal-title":"Curr Opin Plant Biol"},{"issue":"6","key":"pone.0318506.ref002","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.1016\/j.cell.2018.03.044","article-title":"Opposite roles of salicylic acid receptors NPR1 and NPR3\/NPR4 in transcriptional regulation of plant immunity","volume":"173","author":"Y Ding","year":"2018","journal-title":"Cell"},{"issue":"3","key":"pone.0318506.ref003","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1093\/plphys\/kiab166","article-title":"The mobile SAR signal N-hydroxypipecolic acid induces NPR1-dependent transcriptional reprogramming and immune priming","volume":"186","author":"I Yildiz","year":"2021","journal-title":"Plant Physiol"},{"issue":"1","key":"pone.0318506.ref004","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.molcel.2023.11.018","article-title":"NPR1, a key immune regulator for plant survival under biotic and abiotic stresses","volume":"84","author":"R Zavaliev","year":"2024","journal-title":"Mol Cell"},{"issue":"1","key":"pone.0318506.ref005","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1111\/j.1364-3703.2010.00653.x","article-title":"No express or of pathogenesis-related proteins1 (NPR1) and some NPR1-related proteins are sensitive to salicylic acid","volume":"12","author":"F Maier","year":"2011","journal-title":"Mol Plant Pathol"},{"issue":"6","key":"pone.0318506.ref006","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.celrep.2012.05.008","article-title":"The Arabidopsis NPR1 protein is a receptor for the plant defense hormone salicylic acid","volume":"1","author":"Y Wu","year":"2012","journal-title":"Cell Reports"},{"issue":"697","key":"pone.0318506.ref007","first-page":"697","article-title":"Salicylic acid signal transduction: the initiation of biosynthesis, perception and transcriptional reprogramming","volume":"5","author":"C Seyfferth","year":"2014","journal-title":"Front Plant Sci"},{"issue":"8","key":"pone.0318506.ref008","doi-asserted-by":"crossref","first-page":"2057S","DOI":"10.1093\/jn\/130.8.2057S","article-title":"Food of the gods: Cure for humanity? 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