Publications

Selected Lab Publications

Flooding and Low Oxygen

15. Alam, R., Hummel, M., Locke, A., Jia, Z., Ignaci, C.C.I., Baltazar, M.D., Ismail, A., Septiningsih, E.M. and Bailey-Serres, J. (2020) Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.240

14. Reynoso MA, Kajala K, Bajic M, West DA, Pauluzzi G, Yao A, Hatch K, Zumstein K, Woodhouse M, Rodriguez-Medina J, Sinha N, Brady SM, Deal RB, Bailey-Serres J (2019). Evolutionary flexibility in flooding response circuitry in angiosperms Science 365(6459):1291-1295 https://science.sciencemag.org/content/365/6459/1291

13. Lee TA, Bailey-Serres J. (2019) Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress. Plant Cell. 2019 Sep 13. pii: tpc.00463.2019. doi: 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, Visser EJW, Bailey-Serres J, Theodoulou FL, Hebelstrup KH, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ. Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress. Nat Commun. 2019 Sep 5;10(1):4020. doi: 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, Schuurink RC, Bazin J, Bailey-Serres J, Voesenek LACJ, Sasidharan R. (2018) A stress recovery signaling network for enhanced flooding tolerance in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2018 115(26):E6085-E6094. doi: 10.1073/pnas.1803841115

10. Kretzschmar, T., Pelayo, M.A.F., Trijatmiko, K.R., Gabunada, L.F., Alam, R., Jimenez R., Mendioro, M.S., Slamet-Loedin I.H, Sreenivasulu N., Bailey-Serres J., Ismail, A.M, Mackill, D.J., Septiningsih, E.M. (2015) A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. Nature Plants. DOI: 10.1038/NPLANTS.2015.124

9. Giuntoli, B. *, Lee, S.C.*, Licausi, F., Kosmacz, M., Oosumi, T., van Dongen, J.T., Bailey-Serres, J.+ and Perata, P+. (2014) A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis. PLoS Biol 12(9): e1001950. doi:10.1371/journal.pbio.1001950 *co-first authors; +co-corresponding authors.

8. Fukao, T., Yeung, E. and Bailey-Serres, J. (2012) The submergence tolerance gene, SUB1A, delays leaf senescence under prolonged darkness through hormonal regulation in rice. Plant Physiology. 160:1795–1807.

7. Gibbs, D.J.*, Lee, S.C.*, Isa, N.M., Gramuglia, S., Fukao, T., Bassel, G.W., Correia, C.S, Corbineau, F., Theodoulou, F.L., Bailey-Serres, J.+ and Holdsworth, M.J.+ (2011) Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature 479(7373):415-418. *co-first authors; +co-corresponding authors.

6. Fukao, T., Yeung, E. and Bailey-Serres, J. (2011) The submergence tolerance regulator SUB1A mediates crosstalk between submergence and drought tolerance in rice. 23:412-427.

5. Lee, S.-C., Mustroph, A., Sasidharan, R. Vashisht, D., Pedersen, O., Oosumi, T, Voesenek, L.A.C.J. and Bailey-Serres, J. (2011) Molecular characterization of the submergence response of Arabidopsis thaliana ecotype Columbia. New Phytologist. 190:457–471.

4. Fukao, T. and Bailey-Serres, J. (2008) Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellic acid sensitivity in rice. Proceedings of the National Academy of Sciences, USA. 105(43):16814-16819.

3. Fukao, T., Xu, K, Ronald, P.C. and Bailey-Serres, J. (2006) A variable cluster of ethylene responsive-like factors (ERFs) regulates developmental and metabolic acclimation responses to submergence. Plant Cell. 18(8):2021-2034. Characterization of SUB1A

2. Xu, K., Xu, X., Fukao, T., Canalas, P., Maghirang-Rodriguez, R., Heuer, S., Ismail, A., Bailey-Serres, J., Ronald, PC, Mackill, D.J. (2006) Sub1A is an ethylene responsive-factor-like gene that confers submergence tolerance to rice. Nature, 442:705-708. 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, P.S. and Bailey-Serres, J. (2002) RopGAP4-dependent Rop GTPase rheostat control of Arabidopsis oxygen deprivation tolerance. Science 296(5575):2026-2028.

RNA Biology

15. Thanin Chantarachot, Reed S. Sorenson, Maureen Hummel, Haiyan Ke, Alek T. Kettenburg, Daniel Chen, Karen Aiyetiwa, Katayoon Dehesh, Thomas Eulgem, Leslie E. Sieburth, Julia Bailey-Serres. DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition, Nature Plants. https://doi.org/10.1038/s41477-020-0681-8 Free Read Only Version https://rdcu.be/b5Msy

14. Traubenik S, et al. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs Plant Cell 2020.

13. Reynoso, M.A., Pauluzzi, G.C., Kajala K., Cabanlit, S., Velasco, J., Deal, R. Sinha, N.R., Brady, S.M. and Bailey-Serres, J. (2017) Retooled INTACT for capture of nuclei and its use in high-resolution monitoring of the nuclear transcriptome. Plant Physiology 176(1):270-281. INTACT method

12. Bazin, J., Baerenfaller, K., Gosai, S.J., Gregory, B.D., Crespi, M. and Bailey-Serres, J. (2017) Global analysis of ribosome-associated non-coding RNAs unveils new modes of translational regulation. Proceedings of the National Academy of Sciences, USA. 114(46):E10018-E10027. doi: 10.1073/pnas.1708433114

11. Sorenson, R. and Bailey-Serres, J. (2014) Selective mRNA sequestration by OLIGOURIDYLATE BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis. Proceedings of the National Academy of Sciences, USA. 111(6):2373-2378.

10. Juntawong, P., Girke, T., Bazin, J. and Bailey-Serres, J. (2014) Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis Proceedings of the National Academy of Sciences, USA. 111(1):E203-12.

9. Mustroph, A., Lee, S.C., Oosumi, T., Zanetti, M.E., Yang, H., Ma, K., Yaghoubi-Mashi, A. Fukao, T. and Bailey-Serres, J. (2010) Cross-kingdom comparison of transcriptomic adjustments to low oxygen stress highlights conserved and plant-specific responses. Plant Physiology. 152(3):1484-1500.

8. Branco-Price, C., Kaiser, K.A., Jang, C.J.H, Larive, C.K. and Bailey-Serres, J. (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to hypoxia and reoxygenation in Arabidopsis thaliana. Plant Journal. 56:743–755.

7. Zanetti, M.E., Chang I.-.F, Gong, F.-C., Galbraith D.W., Bailey-Serres, J. (2005) Immuno-affinity purification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiology. 138:624-635. TRAP method

6. Branco-Price, C., Kawaguchi, R., Ferriera, R. and Bailey-Serres, J. (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Annals of Botany. 96:647-660.

5. Kawaguchi, R. and Bailey-Serres, J. (2005) mRNA sequence features responsible for translational regulation in Arabidopsis. Nucleic Acids Research 33(3):955-965.

4. Kawaguchi, R., Girke, T. Bray E.A. and Bailey-Serres, J. (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant Journal. 38:823-839. First Translatome Paper for Plants

3. Barakat, A., Szick-Miranda, K., Chang, I.-F., Guyot, R. Blanc, G., Cooke, R., Delseny R. and Bailey-Serres, J. (2001) The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiol. 127: 398-416.

2. Szick, K., Springer, M. and Bailey-Serres J. (1998) Evolutionary analyses of the 12 kDa acidic ribosomal P-proteins reveal a distinct protein of higher plant ribosomes. Proc. Natl. Acad. Sci. USA, 95: 2378-2383.

1. Fennoy, S.L. and Bailey-Serres J. (1995) Posttranscriptional regulation of gene expression in oxygen-deprived roots of maize. Plant Journal. 7:287-295.

Reviews/Commentaries

11. Bailey-Serres, J. and Voesenek L.A.C.J. (2020) Genetic drivers of high-rise rice. https://www.nature.com/articles/d41586-020-02059-0

10. Akmakjian, G. and Bailey-Serres, J. (2020) Nitrogen-responsive transcription factor kinetics meter plant growth. PNAS Commentary. https://www.pnas.org/content/117/24/13196

9. Lee TA, Bailey-Serres J. (2020) Conserved and nuanced hierarchy of gene regulatory response to hypoxia New Phytol 2020 - DOI: 10.1111/nph.16437 Tansley Insight Review

8. Bailey-Serres J, et al. The Dynamic Kaleidoscope of RNA Biology in Plants Plant Physiol 2020. PMID 31908318 Editoral for the Plant Physiology Focus Issue on RNA Biology

7. Bailey-Serres, J., Parker, J.E., Ainsworth, E.A., Oldroyd, and Schroeder, J.I.,Genetic strategies for improving crop yields. Nature 575, 109–118 (2019) doi:10.1038/s41586-019-1679-0 https://rdcu.be/bWqGF

6. Chantarachot, T and Bailey-Serres, J. (2018) Polysomes, stress granules and processing bodies: a dynamic triumvirate controlling cytoplasmic mRNA fate and function. Plant Physiology. 176(1):254-269

5. Mickelbart, M.V., Hasegawa, P.M. and Bailey-Serres, J. (2015) Abiotic stress tolerance genetic mechanisms that translate to crop yield stability. Nature Reviews Genetics. 16:237-251.

4. Voesenek, L.A.C.J. + and Bailey-Serres, J. + (2015) Flood adaptive traits and processes: an overview. Tansley Review. New Phytologist. 206:53-73.

3. Browning, K.S.+ and Bailey-Serres, J.+ (2015) Mechanisms of mRNA translation. The Arabidopsis Book. 13: e0176. BioOne Online Journals. http://dx.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.J. (2010) Submergence tolerant rice: SUB1's journey from landrace to modern cultivar. Rice. 3:138-147.

1. Bailey-Serres, J. and Voesenek, L.A.C.J. (2008) Flooding stress: Acclimations and genetic diversity. Annual Review of Plant Biology. 59:313-339.