Xylem cells rapidly sense and respond to nitrate to promote expansion

Xylem cells rapidly sense and respond to nitrate to promote expansion | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Xylem cells rapidly sense and respond to nitrate to promote expansion S Choudhary, A Renström, T Kochakarn, E Piombo, P Miskolczi, S Jämtgård, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7685028/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Nitrate, beyond being an important plant nutrient, serves as a signaling molecule. During vascular development, nitrate stimulates xylem cell expansion and suppresses xylem maturation, but the underlying signaling has remained unclear. In this study, we explored nitrate signaling during vascular development by monitoring transcriptomic changes in developing xylem tissues in a time series after administering potassium nitrate directly to the xylem sap in hybrid aspen ( Populus tremula x P. tremuloides ) trees. Gene expression analysis revealed a dynamic response, with gene expression being transiently activated at two hours post-application for genes related to xylem expansion and at four to eight hours for genes related to xylem maturation. The two-hour timepoint was therefore selected to examine nitrate mediated cell expansion in expanding xylem elements isolated from the surface of the woody tissue. Using microfluidics coupled with single cell RNA-sequencing (scRNA-seq), we found that majority of the xylem cells could sense and respond to nitrate, and that the cells having the strongest response included both xylem fibers and vessel elements at the earliest stages of cell expansion. Among the candidate transcription factors mediating the nitrate-driven xylem cell expansion we discovered the Populus CYTOKININ RESPONSE FACTOR 4 (CRF4 ). Overexpression of the P. tremula CRF4 in hybrid aspen mimicked the stimulatory effect of nitrate on xylem cell expansion, supporting the function of CRF4 in nitrate-mediated xylem cell expansion. Taken together, we identified a coordinated, system-wide response to nitrate whereby nitrate is rapidly and transiently sensed in most of the xylem elementsand provide evidence for nitrate being taken up from the xylem sap into the ray parenchyma and regulate early xylem development through transcriptional circuits unique to xylem cells. Full Text Additional Declarations The authors declare no competing interests. Supplementary Files TableS1.xlsx Additional file 1: Table S1 Supplementary data from the time course RNA-seq experiment. TableS2.xlsx Additional file 2: Table S2 Supplementary data from the scRNA-seq experiment. TableS3.xlsx Additional file 3: Table S3 Differentially expressed genes (DEGs) of this study that were reported nitrate responsive in earlier studies in literature. Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7685028","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":521049304,"identity":"8b261168-c896-493e-9bdf-b33b65bccd52","order_by":0,"name":"S Choudhary","email":"","orcid":"","institution":"Swedish University of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"S","middleName":"","lastName":"Choudhary","suffix":""},{"id":521049305,"identity":"1e16c74f-578f-4db3-b223-b1add9dd99a1","order_by":1,"name":"A Renström","email":"","orcid":"","institution":"Swedish University of Agricultural 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expansion\u003c/strong\u003e\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research 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During vascular development, nitrate stimulates xylem cell expansion and suppresses xylem maturation, but the underlying signaling has remained unclear. In this study, we explored nitrate signaling during vascular development by monitoring transcriptomic changes in developing xylem tissues in a time series after administering potassium nitrate directly to the xylem sap in hybrid aspen (\u003cem\u003ePopulus tremula\u003c/em\u003e x \u003cem\u003eP. tremuloides\u003c/em\u003e) trees. Gene expression analysis revealed a dynamic response, with gene expression being transiently activated at two hours post-application for genes related to xylem expansion and at four to eight hours for genes related to xylem maturation. The two-hour timepoint was therefore selected to examine nitrate mediated cell expansion in expanding xylem elements isolated from the surface of the woody tissue. Using microfluidics coupled with single cell RNA-sequencing (scRNA-seq), we found that majority of the xylem cells could sense and respond to nitrate, and that the cells having the strongest response included both xylem fibers and vessel elements at the earliest stages of cell expansion. Among the candidate transcription factors mediating the nitrate-driven xylem cell expansion we discovered the \u003cem\u003ePopulus\u003c/em\u003e \u003cem\u003eCYTOKININ RESPONSE FACTOR 4\u003c/em\u003e \u003cem\u003e(CRF4\u003c/em\u003e). Overexpression of the \u003cem\u003eP. tremula\u003c/em\u003e \u003cem\u003eCRF4\u003c/em\u003e in hybrid aspen mimicked the stimulatory effect of nitrate on xylem cell expansion, supporting the function of CRF4 in nitrate-mediated xylem cell expansion. Taken together, we identified a coordinated, system-wide response to nitrate whereby nitrate is rapidly and transiently sensed in most of the xylem elementsand provide evidence for nitrate being taken up from the xylem sap into the ray parenchyma and regulate early xylem development through transcriptional circuits unique to xylem cells.\u003c/p\u003e","manuscriptTitle":"Xylem cells rapidly sense and respond to nitrate to promote expansion","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2025-10-28 21:55:44","doi":"10.21203/rs.3.rs-7685028/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2025-09-26 10:24:57","doi":"10.21203/rs.3.rs-7685028/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"0fd0e27a-6711-4b85-aa3b-8f3f80fccc78","owner":[],"postedDate":"October 28th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-10-02T12:53:50+00:00","versionOfRecord":[],"versionCreatedAt":"2025-10-28 21:55:44","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-7685028","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7685028","identity":"rs-7685028","version":["v2"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}