Embedded Files
Selected Lab Publications
Selected Lab Publications
Water Extremes, including flooding and drought
Water Extremes, including flooding and drought
3. Manzano C, Morimoto KW, Shaar-Moshe L, Mason GA, Cantó-Pastor A, Gouran M, De Bellis D, Ursache R, Kajala K, Sinha N, et al. Regulation and function of a polarly localized lignin barrier in the exodermis. Nat Plants. 2024:11(1):118–130. https://doi.org/10.1038/s41477-024-01864-z
2. Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, et al. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Developmental Cell. 2022:57(9):1177-1192.e6. https://doi.org/10.1016/j.devcel.2022.04.013
1. Fukao T, Yeung E, and Bailey-Serres J. The Submergence Tolerance Regulator SUB1A Mediates Crosstalk between Submergence and Drought Tolerance in Rice. The Plant Cell. 2011:23(1):412–427. https://doi.org/10.1105/tpc.110.080325
Flooding and Low Oxygen
Flooding and Low Oxygen
15. Alam R, Hummel M, Yeung E, Locke AM, Ignacio JCI, Baltazar MD, Jia Z, Ismail AM, Septiningsih EM, and Bailey‐Serres J. Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct. 2020:4(7):e00240. https://doi.org/10.1002/pld3.240
14. Reynoso MA, Kajala K, Bajic M, West DA, Pauluzzi G, Yao AI, Hatch K, Zumstein K, Woodhouse M, Rodriguez-Medina J, et al. Evolutionary flexibility in flooding response circuitry in angiosperms. Science. 2019:365(6459):1291–1295. https://doi.org/10.1126/science.aax8862
13. Lee TA and Bailey-Serres J. Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress. Plant Cell. 2019:tpc.00463.2019. https://doi.org/10.1105/tpc.19.00463
12. Hartman S, Liu Z, Van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, Van Dongen N, Bosman F, Bassel GW, et al. Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress. Nat Commun. 2019:10(1):4020. https://doi.org/10.1038/s41467-019-12045-4
Utrecht University Flooding Team (Plant Ecophysiology Group)
11. Yeung E, Van Veen H, Vashisht D, Sobral Paiva AL, Hummel M, Rankenberg T, Steffens B, Steffen-Heins A, Sauter M, De Vries M, et al. A stress recovery signaling network for enhanced flooding tolerance in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2018:115(26). https://doi.org/10.1073/pnas.1803841115
10. Kretzschmar T, Pelayo MAF, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, et al. A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. Nature Plants. 2015:1(9):15124. https://doi.org/10.1038/nplants.2015.124
9. Giuntoli B, Lee SC, Licausi F, Kosmacz M, Oosumi T, Van Dongen JT, Bailey-Serres J, and Perata P. A Trihelix DNA Binding Protein Counterbalances Hypoxia-Responsive Transcriptional Activation in Arabidopsis. PLoS Biol. 2014:12(9):e1001950. https://doi.org/10.1371/journal.pbio.1001950
8. Fukao T, Yeung E, and Bailey-Serres J. The Submergence Tolerance Gene SUB1A Delays Leaf Senescence under Prolonged Darkness through Hormonal Regulation in Rice. Plant Physiology. 2012:160(4):1795–1807. https://doi.org/10.1104/pp.112.207738
7. Gibbs DJ, Lee SC, Md Isa N, Gramuglia S, Fukao T, Bassel GW, Correia CS, Corbineau F, Theodoulou FL, Bailey-Serres J, et al. Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature. 2011:479(7373):415–418. https://doi.org/10.1038/nature10534
6. Fukao T, Yeung E, and Bailey-Serres J. The Submergence Tolerance Regulator SUB1A Mediates Crosstalk between Submergence and Drought Tolerance in Rice. The Plant Cell. 2011:23(1):412–427. https://doi.org/10.1105/tpc.110.080325
5. Lee SC, Mustroph A, Sasidharan R, Vashisht D, Pedersen O, Oosumi T, Voesenek LACJ, and Bailey‐Serres J. Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia. New Phytologist. 2011:190(2):457–471. https://doi.org/10.1111/j.1469-8137.2010.03590.x
4. Fukao T and Bailey-Serres J. Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc Natl Acad Sci USA. 2008:105(43):16814–16819. https://doi.org/10.1073/pnas.0807821105
3. Fukao T, Xu K, Ronald PC, and Bailey-Serres J. A Variable Cluster of Ethylene Response Factor–Like Genes Regulates Metabolic and Developmental Acclimation Responses to Submergence in Rice. The Plant Cell. 2006:18(8):2021–2034. https://doi.org/10.1105/tpc.106.043000
Characterization of SUB1A
2. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, and Mackill DJ. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature. 2006:442(7103):705–708. https://doi.org/10.1038/nature04920
Awarded the CGIAR Science Award for Outstanding Scientific Article in 2006 by the Consultative Group on International Agricultural Research.
Characterization of SUB1A
1. Baxter-Burrell A, Yang Z, Springer PS, and Bailey-Serres J. RopGAP4-Dependent Rop GTPase Rheostat Control of Arabidopsis Oxygen Deprivation Tolerance. Science. 2002:296(5575):2026–2028. https://doi.org/10.1126/science.1071505
RNA Biology
RNA Biology
16. Chantarachot T, Sorenson RS, Hummel M, Ke H, Kettenburg AT, Chen D, Aiyetiwa K, Dehesh K, Eulgem T, Sieburth LE, et al. DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs. Nat Plants. 2020:6(6):675–685. https://doi.org/10.1038/s41477-020-0681-8
Free Read Only Version https://rdcu.be/b5Msy
15. Traubenik S, Reynoso MA, Hobecker K, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco F, and Zanetti ME. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs. Plant Cell. 2020:32(2):352–373. https://doi.org/10.1105/tpc.19.00647
14. Reynoso MA, Pauluzzi GC, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal R, Sinha NR, Brady SM, and Bailey-Serres J. Nuclear Transcriptomes at High Resolution Using Retooled INTACT. Plant Physiol. 2018:176(1):270–281. https://doi.org/10.1104/pp.17.00688
INTACT method
13. Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, and Bailey-Serres J. Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci USA. 2017:114(46). https://doi.org/10.1073/pnas.1708433114
12. Sorenson R and Bailey-Serres J. Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis. Proc Natl Acad Sci USA. 2014:111(6):2373–2378. https://doi.org/10.1073/pnas.1314851111
11. Juntawong P, Girke T, Bazin J, and Bailey-Serres J. Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci USA. 2014:111(1). https://doi.org/10.1073/pnas.1317811111
10. Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, and Bailey-Serres J. Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses. Plant Physiology. 2010:152(3):1484–1500. https://doi.org/10.1104/pp.109.151845
9. Mustroph A, Zanetti ME, Jang CJH, Holtan HE, Repetti PP, Galbraith DW, Girke T, and Bailey-Serres J. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci USA. 2009:106(44):18843–18848. https://doi.org/10.1073/pnas.0906131106
TRAP method for cell- and region-specific translatomes. See Methods page for seeds, constructs, methods.
8. Branco‐Price C, Kaiser KA, Jang CJH, Larive CK, and Bailey‐Serres J. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. The Plant Journal. 2008:56(5):743–755. https://doi.org/10.1111/j.1365-313X.2008.03642.x
7. Zanetti ME, Chang I-F, Gong F, Galbraith DW, and Bailey-Serres J. Immunopurification of Polyribosomal Complexes of Arabidopsis for Global Analysis of Gene Expression. Plant Physiology. 2005:138(2):624–635. https://doi.org/10.1104/pp.105.059477
TRAP method
6. Branco-Price C, Kawaguchi R, Ferreira RB, and Bailey-Serres J. Genome-wide Analysis of Transcript Abundance and Translation in Arabidopsis Seedlings Subjected to Oxygen Deprivation. Annals of Botany. 2005:96(4):647–660. https://doi.org/10.1093/aob/mci217
5. Kawaguchi R, and Bailey-Serres J. mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Research. 2005:33(3):955–965. https://doi.org/10.1093/nar/gki240
4. Kawaguchi R, Girke T, Bray EA, and Bailey‐Serres J. Differential mRNA translation contributes to gene regulation under non‐stress and dehydration stress conditions in Arabidopsis thaliana. The Plant Journal. 2004:38(5):823–839. https://doi.org/10.1111/j.1365-313X.2004.02090.x
First Translatome Paper for Plants
3. Barakat A, Szick-Miranda K, Chang I-F, Guyot R, Blanc G, Cooke R, Delseny M, and Bailey-Serres J. The Organization of Cytoplasmic Ribosomal Protein Genes in the Arabidopsis Genome. Plant Physiology. 2001:127(2):398–415. https://doi.org/10.1104/pp.010265
2. Szick K, Springer M, and Bailey-Serres J. Evolutionary analyses of the 12-kDa acidic ribosomal P-proteins reveal a distinct protein of higher plant ribosomes. Proc Natl Acad Sci USA. 1998:95(5):2378–2383. https://doi.org/10.1073/pnas.95.5.2378
1. Fennoy SL and Bailey‐Serres J. Post‐transcriptional regulation of gene expression in oxygen‐deprived roots of maize. The Plant Journal. 1995:7(2):287–295. https://doi.org/10.1046/j.1365-313X.1995.7020287.x
Reviews/Commentaries
Reviews/Commentaries
13. Zafar SA and Bailey-Serres J. Decoding the evolution of C4 photosynthesis. Trends in Plant Science. 2025:S1360138525000421. https://doi.org/10.1016/j.tplants.2025.02.008
12. Ashikari M, Nagai K, and Bailey-Serres J. Surviving floods: Escape and quiescence strategies of rice coping with submergence. Plant Physiology. 2025:197(2):kiaf029. https://doi.org/10.1093/plphys/kiaf029
11. Bailey-Serres J and Voesenek LACJ. Genetic drivers of high-rise rice that survives deep floods. Nature. 2020:584(7819):44–45. https://doi.org/10.1038/d41586-020-02059-0
10. Akmakjian GZ and Bailey-Serres J. Nitrogen-responsive transcription factor kinetics meter plant growth. Proc Natl Acad Sci USA. 2020:117(24):13196–13198. https://doi.org/10.1073/pnas.2007441117
9. Lee TA and Bailey‐Serres J. Conserved and nuanced hierarchy of gene regulatory response to hypoxia. New Phytologist. 2021:229(1):71–78. https://doi.org/10.1111/nph.16437
Tansley Insight Review
8. Bailey-Serres J, Zhai J, and Seki M. The Dynamic Kaleidoscope of RNA Biology in Plants. Plant Physiol. 2020:182(1):1–9. https://doi.org/10.1104/pp.19.01558
Editoral for the Plant Physiology Focus Issue on RNA Biology
7. Bailey-Serres J, Parker JE, Ainsworth EA, Oldroyd GED, and Schroeder JI. Genetic strategies for improving crop yields. Nature. 2019:575(7781):109–118. https://doi.org/10.1038/s41586-019-1679-0
Free to view: https://rdcu.be/bWqGF
6. Chantarachot T and Bailey-Serres J. Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function. Plant Physiol. 2018:176(1):254–269. https://doi.org/10.1104/pp.17.01468
5. Mickelbart MV, Hasegawa PM, and Bailey-Serres J. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet. 2015:16(4):237–251. https://doi.org/10.1038/nrg3901
4. Voesenek LACJ and Bailey‐Serres J. Flood adaptive traits and processes: an overview. New Phytologist. 2015:206(1):57–73. https://doi.org/10.1111/nph.13209
Tansley Insight Review
3. Browning KS+ and Bailey-Serres J+. Mechanism of Cytoplasmic mRNA Translation. The Arabidopsis Book. 2015:13:e0176. https://doi.org/10.1199/tab.0176
+co-corresponding authors (Invited)
2. Bailey-Serres J, Fukao T, Ronald P, Ismail A, Heuer S, and Mackill D. Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar. Rice. 2010:3(2–3):138–147. https://doi.org/10.1007/s12284-010-9048-5
1. Bailey-Serres J and Voesenek LACJ. Flooding Stress: Acclimations and Genetic Diversity. Annu Rev Plant Biol. 2008:59(1):313–339. https://doi.org/10.1146/annurev.arplant.59.032607.092752
Editorials
Editorials
1. Gibbs DJ, Theodoulou FL, and Bailey-Serres J. Primed to persevere: Hypoxia regulation from epigenome to protein accumulation in plants. Plant Physiology. 2024:197(1):kiae584. https://doi.org/10.1093/plphys/kiae584
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