{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T22:52:21Z","timestamp":1789599141787,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011218","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,4,3]],"date-time":"2023-04-03T00:00:00Z","timestamp":1680480000000}}],"reference-count":73,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T00:00:00Z","timestamp":1679443200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2021-70410-35297"],"award-info":[{"award-number":["2021-70410-35297"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R35GM143067"],"award-info":[{"award-number":["R35GM143067"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>In plants, age-related resistance (ARR) refers to a gain of disease resistance during shoot or organ maturation. ARR associated with vegetative phase change, a transition from juvenile to adult stage, is a widespread agronomic trait affecting resistance against multiple pathogens. How innate immunity in a plant is differentially regulated during successive stages of shoot maturation is unclear. In this work, we found that <jats:italic>Arabidopsis thaliana<\/jats:italic> showed ARR against its bacterial pathogen <jats:italic>Pseudomonas syringae pv<\/jats:italic>. <jats:italic>tomato<\/jats:italic> DC3000 during vegetative phase change. The timing of the ARR activation was associated with a temporal drop of miR156 level. The microRNA miR156 maintains juvenile phase by inhibiting the accumulation and translation of <jats:italic>SPL<\/jats:italic> transcripts. A systematic inspection of the loss- and gain-of-function mutants of 11 <jats:italic>SPL<\/jats:italic> genes revealed that a subset of <jats:italic>SPL<\/jats:italic> genes, notably <jats:italic>SPL2<\/jats:italic>, <jats:italic>SPL10<\/jats:italic>, and <jats:italic>SPL11<\/jats:italic>, activated ARR in adult stage. The immune function of SPL10 was independent of its role in morphogenesis. Furthermore, the SPL10 mediated an age-dependent augmentation of the salicylic acid (SA) pathway partially by direct activation of <jats:italic>PAD4<\/jats:italic>. Disrupting SA biosynthesis or signaling abolished the ARR against <jats:italic>Pto<\/jats:italic> DC3000. Our work demonstrated that the miR156-SPL10 module in <jats:italic>Arabidopsis<\/jats:italic> is deployed to operate immune outputs over developmental timing.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011218","type":"journal-article","created":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T17:36:45Z","timestamp":1679506605000},"page":"e1011218","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["Distinct function of SPL genes in age-related resistance in Arabidopsis"],"prefix":"10.1371","volume":"19","author":[{"given":"Lanxi","family":"Hu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Qi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Peper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Yao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3665-544X","authenticated-orcid":true,"given":"Li","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,3,22]]},"reference":[{"issue":"5","key":"ppat.1011218.ref001","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.immuni.2006.05.003","article-title":"Aging 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Poethig","year":"2013"},{"issue":"1","key":"ppat.1011218.ref011","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/403567","article-title":"Phase change in higher plants and somatic cell heredity","volume":"37","author":"RA Brink","year":"1962","journal-title":"The Quarterly Review of Biology"},{"issue":"4983","key":"ppat.1011218.ref012","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1126\/science.250.4983.923","article-title":"Phase change and the regulation of shoot morphogenesis in plants","volume":"250","author":"RS Poethig","year":"1990","journal-title":"Science"},{"issue":"2","key":"ppat.1011218.ref013","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1094\/PHYTO-04-19-0128-R","article-title":"Changes in winter squash fruit exocarp structure associated with age-related resistance to Phytophthora capsici","volume":"110","author":"SA Alzohairy","year":"2020","journal-title":"Phytopathology"},{"key":"ppat.1011218.ref014","doi-asserted-by":"crossref","first-page":"775","DOI":"10.3389\/fpls.2014.00775","article-title":"Some things get better with age: differences in salicylic acid accumulation and defense signaling in young and mature Arabidopsis.","volume":"5","author":"P Carella","year":"2015","journal-title":"Frontiers in plant science"},{"issue":"2","key":"ppat.1011218.ref015","doi-asserted-by":"crossref","first-page":"e1002012","DOI":"10.1371\/journal.pgen.1002012","article-title":"miRNA control of vegetative phase change in trees","volume":"7","author":"J-W Wang","year":"2011","journal-title":"PLoS Genet"},{"issue":"3","key":"ppat.1011218.ref016","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1016\/j.jmb.2005.07.013","article-title":"Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains","volume":"352","author":"RP 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Wu","year":"2006","journal-title":"Development"},{"issue":"4","key":"ppat.1011218.ref020","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1016\/j.cell.2009.06.031","article-title":"The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis","volume":"138","author":"G Wu","year":"2009","journal-title":"Cell"},{"issue":"4","key":"ppat.1011218.ref021","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1111\/j.1365-313X.2006.02983.x","article-title":"The miRNA156\/157 recognition element in the 3\u2032 UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings","volume":"49","author":"M Gandikota","year":"2007","journal-title":"The Plant Journal"},{"issue":"5","key":"ppat.1011218.ref022","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.molp.2015.01.008","article-title":"The miR156\/SPL module, a regulatory hub and versatile toolbox, gears up crops for enhanced agronomic 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Cardon","year":"1999","journal-title":"Gene"},{"key":"ppat.1011218.ref026","article-title":"SQUINT Positively Regulates Resistance to the Pathogen Botrytis cinerea via miR156\u2013SPL9 Module in Arabidopsis","author":"T Sun","year":"2022","journal-title":"Plant and Cell Physiology"},{"key":"ppat.1011218.ref027","article-title":"miR156\/SPL9 Regulates Reactive Oxygen Species Accumulation and Immune Response in Arabidopsis thaliana","author":"H Yin","year":"2019","journal-title":"Phytopathology.PHYTO-08-18-0306-R"},{"issue":"6","key":"ppat.1011218.ref028","doi-asserted-by":"crossref","first-page":"2364","DOI":"10.1073\/pnas.1817233116","article-title":"Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone cross-talk","volume":"116","author":"ML Berens","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"20","key":"ppat.1011218.ref029","doi-asserted-by":"crossref","first-page":"6340","DOI":"10.1093\/jxb\/eraa347","article-title":"Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age","volume":"71","author":"A Kanojia","year":"2020","journal-title":"Journal of experimental botany"},{"key":"ppat.1011218.ref030","doi-asserted-by":"crossref","first-page":"17022","DOI":"10.1038\/hortres.2017.22","article-title":"Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici","volume":"4","author":"BN Mansfeld","year":"2017","journal-title":"Hortic Res"},{"issue":"1","key":"ppat.1011218.ref031","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-020-07040-9","article-title":"Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance to Phytophthora capsici in cucumber fruit","volume":"21","author":"BN Mansfeld","year":"2020","journal-title":"BMC genomics"},{"issue":"3","key":"ppat.1011218.ref032","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/s11103-013-0083-7","article-title":"The floral transition is not the developmental switch that confers competence for the Arabidopsis age-related resistance response to Pseudomonas syringae pv. tomato","volume":"83","author":"DC Wilson","year":"2013","journal-title":"Plant Mol Biol"},{"issue":"5","key":"ppat.1011218.ref033","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1111\/j.1364-3703.2009.00557.x","article-title":"Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana","volume":"10","author":"JL Carviel","year":"2009","journal-title":"Mol Plant Pathol"},{"issue":"4","key":"ppat.1011218.ref034","doi-asserted-by":"crossref","first-page":"e1007337","DOI":"10.1371\/journal.pgen.1007337","article-title":"Threshold-dependent repression of SPL gene expression by miR156\/miR157 controls vegetative phase change in Arabidopsis thaliana.","volume":"14","author":"J He","year":"2018","journal-title":"PLoS Genet"},{"issue":"8","key":"ppat.1011218.ref035","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/ng2079","article-title":"Target mimicry provides a new mechanism for regulation of microRNA activity","volume":"39","author":"JM Franco-Zorrilla","year":"2007","journal-title":"Nature genetics"},{"issue":"1\u20132","key":"ppat.1011218.ref036","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gene.2008.03.016","article-title":"Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family","volume":"418","author":"A-Y Guo","year":"2008","journal-title":"Gene"},{"issue":"3","key":"ppat.1011218.ref037","doi-asserted-by":"crossref","first-page":"e1003235","DOI":"10.1371\/journal.ppat.1003235","article-title":"Novel positive regulatory role for the SPL6 transcription factor in the N TIR-NB-LRR receptor-mediated plant innate immunity","volume":"9","author":"MS Padmanabhan","year":"2013","journal-title":"PLoS pathogens"},{"issue":"2","key":"ppat.1011218.ref038","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.devcel.2009.06.007","article-title":"The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1","volume":"17","author":"A Yamaguchi","year":"2009","journal-title":"Developmental cell"},{"issue":"22","key":"ppat.1011218.ref039","doi-asserted-by":"crossref","first-page":"7927","DOI":"10.1093\/jxb\/erab373","article-title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","volume":"72","author":"P Ding","year":"2021","journal-title":"Journal of Experimental Botany"},{"issue":"3","key":"ppat.1011218.ref040","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1242\/dev.124.3.645","article-title":"Phase change and the regulation of trichome distribution in Arabidopsis thaliana","volume":"124","author":"A Telfer","year":"1997","journal-title":"Development"},{"issue":"5","key":"ppat.1011218.ref041","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.tplants.2012.02.010","article-title":"Evolution of jasmonate and salicylate signal crosstalk","volume":"17","author":"JS Thaler","year":"2012","journal-title":"Trends in plant science"},{"issue":"11","key":"ppat.1011218.ref042","doi-asserted-by":"crossref","first-page":"e0142133","DOI":"10.1371\/journal.pone.0142133","article-title":"Exocarp Properties and Transcriptomic Analysis of Cucumber (Cucumis sativus) Fruit Expressing Age-Related Resistance to Phytophthora capsici.","volume":"10","author":"K Ando","year":"2015","journal-title":"PLoS One"},{"issue":"2","key":"ppat.1011218.ref043","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.chom.2017.01.003","article-title":"Pseudomonas syringae Type III Effector HopBB1 Promotes Host Transcriptional Repressor Degradation to Regulate Phytohormone Responses and Virulence.","volume":"21","author":"L Yang","year":"2017","journal-title":"Cell Host Microbe"},{"issue":"6","key":"ppat.1011218.ref044","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":"4","key":"ppat.1011218.ref045","doi-asserted-by":"crossref","first-page":"1802","DOI":"10.1111\/nph.14302","article-title":"A core function of EDS1 with PAD4 is to protect the salicylic acid defense sector in Arabidopsis immunity","volume":"213","author":"H Cui","year":"2017","journal-title":"New Phytologist"},{"issue":"5","key":"ppat.1011218.ref046","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1016\/j.cell.2016.04.038","article-title":"Cistrome and epicistrome features shape the regulatory DNA landscape.","volume":"165","author":"RC O\u2019Malley","year":"2016","journal-title":"Cell"},{"key":"ppat.1011218.ref047","article-title":"Inducible overexpression of Ideal Plant Architecture1 improves both yield and disease resistance in rice","author":"M Liu","year":"2019","journal-title":"Nature plants.1"},{"issue":"6406","key":"ppat.1011218.ref048","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1126\/science.aat7675","article-title":"A single transcription factor promotes both yield and immunity in rice","volume":"361","author":"J Wang","year":"2018","journal-title":"Science"},{"issue":"1","key":"ppat.1011218.ref049","doi-asserted-by":"crossref","first-page":"e1006756","DOI":"10.1371\/journal.ppat.1006756","article-title":"A role for small RNA in regulating innate immunity during plant growth","volume":"14","author":"Y Deng","year":"2018","journal-title":"PLoS pathogens"},{"issue":"7","key":"ppat.1011218.ref050","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1094\/Phyto-83-702","article-title":"Endogenous salicylic acid levels correlate with accumulation of pathogenesis-related proteins and virus resistance in tobacco","volume":"83","author":"N Yalpani","year":"1993","journal-title":"Phytopathology"},{"issue":"11","key":"ppat.1011218.ref051","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1094\/MPMI-07-17-0172-R","article-title":"Age-Related Resistance in Arabidopsis thaliana Involves the MADS-Domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae","volume":"30","author":"DC Wilson","year":"2017","journal-title":"Mol Plant Microbe Interact"},{"issue":"2","key":"ppat.1011218.ref052","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1105\/tpc.010481","article-title":"Age-related resistance in Arabidopsis is a developmentally regulated defense response to Pseudomonas syringae","volume":"14","author":"JV Kus","year":"2002","journal-title":"The Plant Cell"},{"key":"ppat.1011218.ref053","doi-asserted-by":"crossref","first-page":"340","DOI":"10.3389\/fpls.2019.00340","article-title":"Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects.","volume":"10","author":"T Fukao","year":"2019","journal-title":"Front Plant Sci"},{"issue":"1","key":"ppat.1011218.ref054","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/nph.16513","article-title":"Botrytis cinerea induces local hypoxia in Arabidopsis leaves","volume":"229","author":"MC Valeri","year":"2021","journal-title":"New Phytol"},{"issue":"6316","key":"ppat.1011218.ref055","doi-asserted-by":"crossref","first-page":"aaf6395","DOI":"10.1126\/science.aaf6395","article-title":"Intracellular innate immune surveillance devices in plants and animals","volume":"354","author":"JD Jones","year":"2016","journal-title":"Science"},{"issue":"1","key":"ppat.1011218.ref056","doi-asserted-by":"crossref","first-page":"e1004483","DOI":"10.1371\/journal.ppat.1004483","article-title":"Bacterial flagella: twist and stick, or dodge across the kingdoms","volume":"11","author":"Y Rossez","year":"2015","journal-title":"PLoS pathogens."},{"issue":"6772","key":"ppat.1011218.ref057","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1038\/35002607","article-title":"The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans","volume":"403","author":"BJ Reinhart","year":"2000","journal-title":"nature"},{"issue":"3","key":"ppat.1011218.ref058","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/j.devcel.2005.07.009","article-title":"The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans","volume":"9","author":"AL Abbott","year":"2005","journal-title":"Developmental cell"},{"issue":"18","key":"ppat.1011218.ref059","first-page":"E2366","article-title":"Caenorhabditis elegans microRNAs of the let-7 family act in innate immune response circuits and confer robust developmental timing against pathogen stress","volume":"112","author":"Z Ren","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"5736","key":"ppat.1011218.ref060","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1126\/science.1109977","article-title":"Antagonistic control of disease resistance protein stability in the plant immune 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