Plants, including most crops, are intolerant to waterlogging, a stressful condition that limits the oxygen available for roots, thereby inhibiting their growth and functionality. Whether root growth inhibition represents a preventive measure to save energy or is rather a consequence of reduced metabolic rates has yet to be elucidated. In the present study, we gathered evidence for hypoxic repression of root meristem regulators that leads to root growth inhibition. We also explored the contribution of the hormone jasmonic acid (JA) to this process in Arabidopsis thaliana. Analysis of transcriptomic profiles, visualisation of fluorescent reporters and direct hormone quantification confirmed the activation of JA signalling under hypoxia in the roots. Further, root growth assessment in JA-related mutants in aerobic and anaerobic conditions indicated that JA signalling components contribute to active root inhibition under hypoxia. Finally, we show that the oxygen-sensing transcription factor (TF) RAP2.12 can directly induce Jasmonate Zinc-finger proteins (JAZs), repressors of JA signalling, to establish feedback inhibition. In summary, our study sheds new light on active root growth restriction under hypoxic conditions and on the involvement of the JA hormone in this process and its cross talk with the oxygen sensing machinery of higher plants.

Department of Biology University of Pisa 56126 Pisa Italy

Department of Plant Sciences University of Oxford Oxford OX1 3RB UK

Laboratory of Growth Regulators Faculty of Science Palacký University and Institute of Experimental Botany The Czech Academy of Sciences CZ 783 71 Olomouc Czech Republic

Plantlab Institute of Life Sciences Scuola Superiore Sant'Anna 56127 Pisa Italy

The Institute of Agricultural Biology and Biotechnology National Research Council 20133 Milan Italy

See more in PubMed

Akgerman A., Gainer J.L. Diffusion of Gases in Liquids. Ind. Eng. Chem. Fundam. 1972 doi: 10.1021/i160043a016. DOI

Gibbs J., Greenway H. Mechanisms of anoxia tolerance in plants. I. Growth, survival and anaerobic catabolism. Funct. Plant Biol. 2003;30:1–47. doi: 10.1071/PP98095. PubMed DOI

Blokhina O., Fagerstedt K.V. Oxidative metabolism, ROS and NO under oxygen deprivation. Plant Physiol. Biochem. 2010;48:359–373. doi: 10.1016/j.plaphy.2010.01.007. PubMed DOI

van Dongen J.T., Licausi F. Oxygen Sensing and Signaling. Annu. Rev. Plant Biol. 2014;66:150112150216002. doi: 10.1146/annurev-arplant-043014-114813. PubMed DOI

Voesenek L.A.C.J., Bailey-Serres J. Flood adaptive traits and processes: an overview. New Phytol. 2015;206:57–73. doi: 10.1111/nph.13209. PubMed DOI

Mendiondo G.M., Gibbs D.J., Szurman-Zubrzycka M., Korn A., Marquez J., Szarejko I., Maluszynski M., King J., Axcell B., Smart K., et al. Enhanced waterlogging tolerance in barley by manipulation of expression of the N-end rule pathway E3 ligase PROTEOLYSIS6. Plant Biotechnol. J. 2016 doi: 10.1111/pbi.12334. PubMed DOI PMC

Cukrov D., Zermiani M., Brizzolara S., Cestaro A., Licausi F., Luchinat C., Santucci C., Tenori L., Van Veen H., Zuccolo A., et al. Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit. Front. Plant Sci. 2016 doi: 10.3389/fpls.2016.00146. PubMed DOI PMC

Bui L.T., Giuntoli B., Kosmacz M., Parlanti S., Licausi F. Constitutively expressed ERF-VII transcription factors redundantly activate the core anaerobic response in Arabidopsis thaliana. Plant Sci. 2015;236:37–43. doi: 10.1016/j.plantsci.2015.03.008. PubMed DOI

Gasch P., Fundinger M., Müller J.T., Lee T., Bailey-Serres J., Mustroph A. Redundant ERF-VII transcription factors bind an evolutionarily-conserved cis-motif to regulate hypoxia-responsive gene expression in Arabidopsis. Plant Cell. 2015:TPC2015-00866-RA. doi: 10.1105/tpc.15.00866. PubMed DOI PMC

Kosmacz M., Parlanti S., Schwarzländer M., Kragler F., Licausi F., Van Dongen J.T. The stability and nuclear localization of the transcription factor RAP2.12 are dynamically regulated by oxygen concentration. Plant, Cell Environ. 2015;38:1094–1103. doi: 10.1111/pce.12493. PubMed DOI

Gibbs D.J., Lee S.C., Md Isa N., Gramuglia S., Fukao T., Bassel G.W., Correia C.S., Corbineau F., Theodoulou F.L., Bailey-Serres J., et al. Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature. 2011;479:415–418. doi: 10.1038/nature10534. PubMed DOI PMC

Licausi F., Kosmacz M., Weits D.A., Giuntoli B., Giorgi F.M., Voesenek L.A.C.J., Perata P., van Dongen J.T. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature. 2011;479:419–422. doi: 10.1038/nature10536. PubMed DOI

Weits D.A., Giuntoli B., Kosmacz M., Parlanti S., Hubberten H.-M., Riegler H., Hoefgen R., Perata P., van Dongen J.T., Licausi F. Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nat. Commun. 2014;5:3425. doi: 10.1038/ncomms4425. PubMed DOI PMC

White M.D., Klecker M., Hopkinson R.J., Weits D.A., Mueller C., Naumann C., O’Neill R., Wickens J., Yang J., Brooks-Bartlett J.C., et al. Plant cysteine oxidases are dioxygenases that directly enable arginyl transferase-catalysed arginylation of N-end rule targets. Nat. Commun. 2017;8:1–9. doi: 10.1038/ncomms14690. PubMed DOI PMC

White M.D., Kamps J.J.A.G., East S., Taylor Kearney L.J., Flashman E. The plant cysteine oxidases from Arabidopsis thaliana are kinetically tailored to act as oxygen sensors. J. Biol. Chem. 2018;293:11786–11795. doi: 10.1074/jbc.RA118.003496. PubMed DOI PMC

Garzón M., Eifler K., Faust A., Scheel H., Hofmann K., Koncz C., Yephremov A., Bachmair A. PRT6 /At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Lett. 2007;581:3189–3196. doi: 10.1016/j.febslet.2007.06.005. PubMed DOI

Paul M.V., Iyer S., Amerhauser C., Lehmann M., van Dongen J.T., Geigenberger P. RAP2.12 oxygen sensing regulates plant metabolism and performance under both normoxia and hypoxia. Plant Physiol. 2016;172:00460. doi: 10.1104/pp.16.00460. PubMed DOI PMC

Giuntoli B., Shukla V., Maggiorelli F., Giorgi F.M., Lombardi L., Perata P., Licausi F. Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana. Plant. Cell Environ. 2017 doi: 10.1111/pce.13037. PubMed DOI

Wright A.J., de Kroon H., Visser E.J.W., Buchmann T., Ebeling A., Eisenhauer N., Fischer C., Hildebrandt A., Ravenek J., Roscher C., et al. Plants are less negatively affected by flooding when growing in species-rich plant communities. New Phytol. 2017 doi: 10.1111/nph.14185. PubMed DOI

Jitsuyama Y. Morphological root responses of soybean to rhizosphere hypoxia reflect waterlogging tolerance. Can. J. Plant Sci. 2015;95:999–1005. doi: 10.4141/cjps-2014-370. DOI

Cardoso J.A., Jiménez J.D.L.C., Rao I.M. Waterlogging-induced changes in root architecture of germplasm accessions of the tropical forage grass Brachiaria humidicola. AoB Plants. 2014 doi: 10.1093/aobpla/plu017. PubMed DOI PMC

Grzesiak M.T., Ostrowska A., Hura K., Rut G., Janowiak F., Rzepka A., Hura T., Grzesiak S. Interspecific differences in root architecture among maize and triticale genotypes grown under drought, waterlogging and soil compaction. Acta Physiol. Plant. 2014 doi: 10.1007/s11738-014-1691-9. DOI

Cornelious B., Chen P., Chen Y., De Leon N., Shannon J.G., Wang D. Identification of QTLs underlying water-logging tolerance in soybean. Mol. Breed. 2005 doi: 10.1007/s11032-005-5911-2. DOI

Hodge A., Berta G., Doussan C., Merchan F., Crespi M. Plant root growth, architecture and function. Plant Soil. 2009;321:153–187. doi: 10.1007/s11104-009-9929-9. DOI

López-Bucio J., Cruz-Ramírez A., Herrera-Estrella L. The role of nutrient availability in regulating root architecture. Curr. Opin. Plant Biol. 2003;6:280–287. doi: 10.1016/S1369-5266(03)00035-9. PubMed DOI

Lynch J. Root Architecture and Plant Productivity. Plant Physiol. 1995;109:7–13. doi: 10.1104/pp.109.1.7. PubMed DOI PMC

Vidoz M.L., Loreti E., Mensuali A., Alpi A., Perata P. Hormonal interplay during adventitious root formation in flooded tomato plants. Plant J. 2010;63:551–562. doi: 10.1111/j.1365-313X.2010.04262.x. PubMed DOI

Visser E., Cohen J.D., Barendse G., Blom C., Voesenek L. An Ethylene-Mediated Increase in Sensitivity to Auxin Induces Adventitious Root Formation in Flooded Rumex palustris Sm. Plant Physiol. 1996 doi: 10.1104/pp.112.4.1687. PubMed DOI PMC

Joshi R., Kumar P. Lysigenous aerenchyma formation involves non-apoptotic programmed cell death in rice (Oryza sativa L.) roots. Physiol. Mol. Biol. Plants. 2012;18:1. doi: 10.1007/s12298-011-0093-3. PubMed DOI PMC

THOMAS A.L., GUERREIRO S.M.C., SODEK L. Aerenchyma Formation and Recovery from Hypoxia of the Flooded Root System of Nodulated Soybean. Ann. Bot. 2005;96:1191. doi: 10.1093/aob/mci272. PubMed DOI PMC

van Dongen J.T., Fröhlich A., Ramírez-Aguilar S.J., Schauer N., Fernie A.R., Erban A., Kopka J., Clark J., Langer A., Geigenberger P. Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Ann. Bot. 2009;103:269–280. doi: 10.1093/aob/mcn126. PubMed DOI PMC

Mustroph A., Zanetti M.E., Jang C.J.H., Holtan H.E., Repetti P.P., Galbraith D.W., Girke T., Bailey-Serres J. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc. Natl. Acad. Sci. 2009;106:18843–18848. doi: 10.1073/pnas.0906131106. PubMed DOI PMC

Jackson M.B., Fenning T.M., Jenkins W. Aerenchyma (gas-space) formation in adventitious roots of rice (Oryza sativa L.) is not controlled by ethylene or small partial pressures of oxygen. J. Exp. Bot. 1985;36:1566–1572. doi: 10.1093/jxb/36.10.1566. DOI

Voesenek L.A.C.J., Rijnders J.H.G.M., Peeters A.J.M., Van De Steeg H.M., De Kroon H. Plant hormones regulate fast shoot elongation under water: From genes to communities. Ecology. 2004;85:16–27. doi: 10.1890/02-740. DOI

Steffens B., Wang J., Sauter M. Interactions between ethylene, gibberellin and abscisic acid regulate emergence and growth rate of adventitious roots in deepwater rice. Planta. 2006;223:604–612. doi: 10.1007/s00425-005-0111-1. PubMed DOI

Nishiuchi S., Yamauchi T., Takahashi H., Kotula L., Nakazono M. Mechanisms for coping with submergence and waterlogging in rice. Rice. 2012;5:2. doi: 10.1186/1939-8433-5-2. PubMed DOI PMC

Creelman R.A., Mullet J.E. Biosynthesis and Action of Jasmonates in Plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1997;48:355–381. doi: 10.1146/annurev.arplant.48.1.355. PubMed DOI

Staswick P.E. The tryptophan conjugates of jasmonic and indole-3-acetic acids are endogenous auxin inhibitors. Plant Physiol. 2009 doi: 10.1104/pp.109.138529. PubMed DOI PMC

McConn M., Browse J. The Critical Requirement for Linolenic Acid Is Pollen Development, Not Photosynthesis, in an Arabidopsis Mutant. Plant Cell. 1996;8:403–416. doi: 10.2307/3870321. PubMed DOI PMC

Schommer C., Palatnik J.F., Aggarwal P., Chételat A., Cubas P., Farmer E.E., Nath U., Weigel D. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 2008;6:1991–2001. doi: 10.1371/journal.pbio.0060230. PubMed DOI PMC

Xie D. COI1: An Arabidopsis Gene Required for Jasmonate-Regulated Defense and Fertility. Science. 1998;280:1091–1094. doi: 10.1126/science.280.5366.1091. PubMed DOI

Montiel G., Zarei A., Körbes A.P., Memelink J. The jasmonate-responsive element from the ORCA3 promoter from catharanthus roseus is active in arabidopsis and is controlled by the transcription factor AtMYC2. Plant Cell Physiol. 2011;52:578–587. doi: 10.1093/pcp/pcr016. PubMed DOI

Chen Q., Sun J., Zhai Q., Zhou W., Qi L., Xu L., Wang B., Chen R., Jiang H., Qi J., et al. The Basic Helix-Loop-Helix Transcription Factor MYC2 Directly Represses PLETHORA Expression during Jasmonate-Mediated Modulation of the Root Stem Cell Niche in Arabidopsis. Plant Cell Online. 2011;23:3335–3352. doi: 10.1105/tpc.111.089870. PubMed DOI PMC

Sun J., Xu Y., Ye S., Jiang H., Chen Q., Liu F., Zhou W., Chen R., Li X., Tietz O., et al. Arabidopsis ASA1 is important for jasmonate-mediated regulation of auxin biosynthesis and transport during lateral root formation. Plant Cell. 2009;21:1495–1511. doi: 10.1105/tpc.108.064303. PubMed DOI PMC

Petricka J.J., Winter C.M., Benfey P.N. Control of Arabidopsis root development. Annu. Rev. Plant Biol. 2012 doi: 10.1146/annurev-arplant-042811-105501. PubMed DOI PMC

Dathe W., Rönsch H., Preiss A., Schade W., Sembdner G., Schreiber K. Endogenous plant hormones of the broad bean, Vicia faba L. (-)-jasmonic acid, a plant growth inhibitor in pericarp. Planta. 1981;153:530–535. doi: 10.1007/BF00385537. PubMed DOI

Fonseca S., Chini A., Hamberg M., Adie B., Porzel A., Kramell R., Miersch O., Wasternack C., Solano R. (+)-7-iso-Jasmonoyl-L-isoleucine is the endogenous bioactive jasmonate. Nat. Chem. Biol. 2009;5:344–350. doi: 10.1038/nchembio.161. PubMed DOI

Wasternack C., Hause B. Jasmonates: Biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Ann. Bot. 2013;111:1021–1058. doi: 10.1093/aob/mct067. PubMed DOI PMC

Poirier Y., Antonenkov V.D., Glumoff T., Hiltunen J.K. Peroxisomal β-oxidation—A metabolic pathway with multiple functions. Biochim. Biophys. Acta - Mol. Cell Res. 2006;1763:1413–1426. doi: 10.1016/j.bbamcr.2006.08.034. PubMed DOI

Abbas M., Berckhan S., Rooney D.J., Gibbs D.J., Vicente Conde J., Sousa Correia C., Bassel G.W., Marín-De La Rosa N., León J., Alabadí D., et al. Oxygen sensing coordinates photomorphogenesis to facilitate seedling survival. Curr. Biol. 2015;25:1483–1488. doi: 10.1016/j.cub.2015.03.060. PubMed DOI PMC

Pauwels L., Morreel K., De Witte E., Lammertyn F., Van Montagu M., Boerjan W., Inzé D., Goossens A. Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells. Proc. Natl. Acad. Sci. USA. 2008;105:1380–1385. doi: 10.1073/pnas.0711203105. PubMed DOI PMC

Hruz T., Laule O., Szabo G., Wessendorp F., Bleuler S., Oertle L., Widmayer P., Gruissem W., Zimmermann P. Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes. Adv. Bioinformatics. 2008;2008:1–5. doi: 10.1155/2008/420747. PubMed DOI PMC

Pauwels L., Goossens A. The JAZ proteins: a crucial interface in the jasmonate signaling cascade. Plant Cell. 2011;23:3089–3100. doi: 10.1105/tpc.111.089300. PubMed DOI PMC

Eysholdt-Derzso E., Sauter M. Root bending is antagonistically affected by hypoxia and ERF-mediated transcription via auxin signaling. Plant Physiol. 2017;175:412–423. doi: 10.1104/pp.17.00555. PubMed DOI PMC

Yazdanbakhsh N., Fisahn J. Analysis of Arabidopsis thaliana root growth kinetics with high temporal and spatial resolution. Ann. Bot. 2010 doi: 10.1093/aob/mcq048. PubMed DOI PMC

Bannenberg G., Martínez M., Hamberg M., Castresana C. Diversity of the enzymatic activity in the lipoxygenase gene family of arabidopsis thaliana. Lipids. 2009;44:85–95. doi: 10.1007/s11745-008-3245-7. PubMed DOI

Nguyen C.T., Martinoia E., Farmer E.E. Emerging Jasmonate Transporters. Mol. Plant. 2017 doi: 10.1016/j.molp.2017.03.007. PubMed DOI

Li Q., Zheng J., Li S., Huang G., Skilling S.J., Wang L., Li L., Li M., Yuan L., Liu P. Transporter-Mediated Nuclear Entry of Jasmonoyl-Isoleucine Is Essential for Jasmonate Signaling. Mol. Plant. 2017 doi: 10.1016/j.molp.2017.01.010. PubMed DOI

de Marchi R., Sorel M., Mooney B., Fudal I., Goslin K., Kwaśniewska K., Ryan P.T., Pfalz M., Kroymann J., Pollmann S., et al. The N-end rule pathway regulates pathogen responses in plants. Sci. Rep. 2016;6:26020. doi: 10.1038/srep26020. PubMed DOI PMC

Ahmad P., Rasool S., Gul A., Sheikh S.A., Akram N.A., Ashraf M., Kazi A.M., Gucel S. Jasmonates: Multifunctional Roles in Stress Tolerance. Front. Plant Sci. 2016 doi: 10.3389/fpls.2016.00813. PubMed DOI PMC

Huang H., Liu B., Liu L., Song S. Jasmonate action in plant growth and development. J. Exp. Bot. 2017 doi: 10.1093/jxb/erw495. PubMed DOI

Giuntoli B., Lee S.C., Licausi F., Kosmacz M., Oosumi T., van Dongen J.T., Bailey-Serres J., Perata P. A Trihelix DNA Binding Protein Counterbalances Hypoxia-Responsive Transcriptional Activation in Arabidopsis. PLoS Biol. 2014 doi: 10.1371/journal.pbio.1001950. PubMed DOI PMC

Schweizer F., Fernandez-Calvo P., Zander M., Diez-Diaz M., Fonseca S., Glauser G., Lewsey M.G., Ecker J.R., Solano R., Reymond P. Arabidopsis Basic Helix-Loop-Helix Transcription Factors MYC2, MYC3, and MYC4 Regulate Glucosinolate Biosynthesis, Insect Performance, and Feeding Behavior. Plant Cell. 2013;25:3117–3132. doi: 10.1105/tpc.113.115139. PubMed DOI PMC

Mähönen A.P., Ten Tusscher K., Siligato R., Smetana O., Díaz-Triviño S., Salojärvi J., Wachsman G., Prasad K., Heidstra R., Scheres B. PLETHORA gradient formation mechanism separates auxin responses. Nature. 2014;515:125–129. doi: 10.1038/nature13663. PubMed DOI PMC

Larrieu A., Champion A., Legrand J., Lavenus J., Mast D., Brunoud G., Oh J., Guyomarc’h S., Pizot M., Farmer E.E., et al. A fluorescent hormone biosensor reveals the dynamics of jasmonate signalling in plants. Nat. Commun. 2015;6:6043. doi: 10.1038/ncomms7043. PubMed DOI PMC

Armengaud P. EZ-Rhizo software. Plant Signal. Behav. 2009;4:139–141. doi: 10.4161/psb.4.2.7763. PubMed DOI PMC

Pauwels L., Inzé D., Goossens A. Jasmonate-inducible gene: what does it mean? Trends Plant Sci. 2009;14:87–91. doi: 10.1016/j.tplants.2008.11.005. PubMed DOI

Shukla V., Lombardi L., Iacopino S., Pencik A., Novak O., Perata P., Giuntoli B., Licausi F. Endogenous hypoxia in lateral root primordia controls root architecture by antagonizing auxin signaling in Arabidopsis. Mol. Plant. 2019 doi: 10.1016/j.molp.2019.01.007. PubMed DOI

Livak K.J., Schmittgen T.D. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods. 2001;25:402–408. doi: 10.1006/meth.2001.1262. PubMed DOI

Floková K., Tarkowská D., Miersch O., Strnad M., Wasternack C., Novák O. UHPLC–MS/MS based target profiling of stress-induced phytohormones. Phytochemistry. 2014;105:147–157. doi: 10.1016/j.phytochem.2014.05.015. PubMed DOI