Selected publications

(2024)

.- Development of modular geminivirus-based vectors for high cargo expression and gene targeting in plants. Neubauer, M., Volle, K., Ascencio-Ibanez, J-T, Hanley-Bowdoin, L., Stepanova, AN., Alonso, JM. bioRxiv. 2024 doi:https://doi.org/10.1101/2024.06.29.601216

.- Arabidopsis as a model for translational research. Yaschenko AE, Alonso JM, Stepanova AN.  Plant Cell. 2024 Feb 27:koae065. doi: 10.1093/plcell/koae065. Online ahead of print.

.- A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters. Fernandez-Moreno JP, Yaschenko AE, Neubauer M, Marchi AJ, Zhao C, Ascencio-Ibanez JT, Alonso JM, Stepanova AN. Plant Biotechnol J. 2024 Jul;22(7):1942-1956. doi: 10.1111/pbi.14313. Epub 2024 Feb 21.

.- Sourcing DNA parts for synthetic biology applications in plants. Vollen, K., Zhao, C., Alonso, JM., Stepanova, AN. Curr Opin Plant Biol. 2024. doi.org/10.1016/j.copbio.2024.103140

(2022)

-. A Ribo-Seq Method to Study Genome-Wide Translational Regulation in Plants. Chen, H., JM., Stepanova, AN. Methods Mol Biol. 2022; 2494:61-98. doi: 10.1007/978-1-0716-2297-1_6.

-. Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help? Yaschenko, A.E., Fenech, M., Mazzoni-Putman, S., Alonso, J.M., Stepanova, A.N. Curr Opin Plant Biol. 2022 Jun 11;68:102241. doi: 10.1016/j.pbi.2022.102241.

 

(2020)

-. Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis. Gomez, MD., Barro-Trastoy, D., Fuster-Almunia, C., Tornero, P., Alonso, JM., Perez-Amador, MA. J Exp Bot. 2020 Dec 31;71(22):7059-7072. doi: 10.1093/jxb/eraa395.

-. Development of a relative quantification method for infrared matrix‐assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings. Bagley, MC., Stepanova, AN., Ekelöf, M., Alonso, JM., Muddiman, DC. Rapid Communications in Mass Spectrometry. https://doi.org/10.1002/rcm.8616

-. Structure-function analysis of interallelic complementation in ROOTY transheterozygotes. Brumos, J., Bobay, BG., Clark, CA., Alonso, JM., Stepanova AN. Plant Physiology. DOI: https://doi.org/10.1104/pp.20.00310

-. Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms. Barro‐Trastoy, D., Carrera, E., Baños, J.,  Palau‐Rodríguez, J.,  Ruiz‐Rivero, O., Tornero, P., Alonso, JM., López‐Díaz, I.,  Gómez, MD., Pérez‐Amador, MA.. Plant Journal. https://doi.org/10.1111/tpj.14684

-. An improved recombineering toolset for plants. Javier Brumos, Chengsong Zhao, Yan Gong, David Soriano, Arjun P Patel, Miguel A Perez-Amador, Anna N Stepanova, Jose M Alonso. Plant Cell. 32 (1), 100-122 (2020). DOI: https://doi.org/10.1105/tpc.19.0043

(2019)  

-. Monitoring Ethylene in Plants: Genetically Encoded Reporters and Biosensors. Josefina‐Patricia Fernandez‐Moreno Anna N. Stepanova. Small Methods. https://doi.org/10.1002/smtd.201900260 (2019)

-. RiboStreamR: a web application for quality-control, analysis, and visualization of Ribo-seq data. Patrick Perkins, Serina Mazzoni-Putman, Anna Stepanova, Jose Alonso and Steffen Heber. BMC Genomics. 2019,20(Suppl 5):422https://doi.org/10.1186/s12864-019-5700-7 (2019)

-.  From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration. Stepanova AN, Alonso JM. Plant Cell. 31 (7) 1393-1394.  DOI: https://doi.org/10.1105/tpc.19.00339 (2019)

-.  RGL2 controls flower development, ovule number and fertility in Arabidopsis. Gómez MD, Fuster-Almunia C, Ocaña-Cuesta J, Alonso JM, Pérez-Amador MA. Plant Sci. 2019 Apr;281:82-92. doi: 10.1016/j.plantsci.2019.01.014. (2019)

(2018)  

-.  Local Auxin Biosynthesis Is a Key Regulator of Plant Development. Brumos J, Robles LM, Yun J, Vu TC, Jackson S, Alonso JM and Stepanova AN. Dev Cell. 47(3):306. DOI:https://doi.org/10.1016/j.devcel.2018.09.022 (2018)

-. Gibberellins negatively modulate ovule number in plants. Gomez MD, Barro-Trastoy D, Escoms E, Saura-Sánchez M, Sánchez I, Briones-Moreno A, Vera-Sirera F, Carrera E, Ripoll JJ, Yanofsky MF, Lopez-Diaz I, Alonso JM, Perez-Amador MA. Development. 145(13). doi: 10.1242/dev.163865. (2018)

-. A plant biologist’s toolbox to study translation. Mazzoni-Putman S and Stepanova AN. Front Plant Sci. 9:873. doi: 10.3389/fpls.2018.00873. eCollection (2018).

-. A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Bhosale et al. (2018). Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R. Nature Communications. 9(1):1409. doi: 10.1038 (2018)

-.Microtubule-Dependent Confinement of a Cell Signaling and Actin Polymerization Control Module Regulates Polarized Cell Growth. Yanagisawa M, Alonso JM, Szymanski DB. Curr Biol. 28(15):2459. DOI: 10.1016/j.cub.2018.05.076 (2018)

(2017)  

-.The Triple Response Assay and Its Use to Characterize Ethylene Mutants in Arabidopsis. Merchante C, Stepanova AN. Methods Mol Biol. 1573:163-209. doi: 10.1007/978-1-4939-6854-1_13. (2017)

-. Relevance of Translational Regulation on Plant Growth and Environmental Responses. Ferrando A, Castellano MM, Lisón P, Leister D, Stepanova AN, Hanson J. Front Plant Sci. 19 (8). (2017)

-.Transcriptional analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle. Estrada-Johnson, E., Csukasi, F., Pizarro, C.M., Vallarino, J.G., Kyriakova, Y., Vioque, A., Brumos, J., Medina-Escobar, N., Botella, M.A., Alonso, J.M., Fernie, A.R., Sanchez-Sevilla, J.F., Osorio, S., Valpuesta, V. Front. Plant Sci. Jul 24;8:1305 (2017)

-. Translational regulation in plants: an interesting past, an exciting present and a promising future. Merchante, C., Stepanova, A.N., and Alonso, J.M. Plant J. 90:628-653 (2017)

(2016)  

-.Cutting out the middle man in light-hormone interactions. Stepanova, A.N. and Alonso, J.M. Dev. Cell 39:524-526 (2016)

-.Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana. Hu, Q., Merchante, C., Stepanova, A.N., Alonso, J.M., Heber, S. IEEE Trans Nanobioscience 15:148-157 (2016)

-.A Ribosome Footprinting Protocol for Plants. Merchante, C., Hu, Q., Heber, S., Alonso, J. and Stepanova, A. N. Bio-protocol 6(21): e1985. (2016)

-.Auxin catabolism unplugged: Role of IAA oxidation in auxin homeostasis. Stepanova AN, Alonso JM. PNAS 113(39):10742-4 (2016)

(2015)  

-.Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2. Merchante, C., Brumos, J., Yun, J., Hu, Q., Spencer, K.R., Enríquez, P., Binder, B.M., Heber, S., Stepanova, A.N., Alonso, J.M. Cell. 163(3):684-97 (2015)

-.50 years of Arabidopsis research: highlights and future directions. Provart, N.J., Alonso, J., Assmann, S.M., Bergmann, D., Brady, S.M., Brkljacic, J., Browse, J., Chapple, C., Colot, V., Cutler, S., Dangl, J., Ehrhardt, D., Friesner, J.D., Frommer, W.B., Grotewold, E., Meyerowitz, E., Nemhauser, J., Nordborg, M., Pikaard, C., Shanklin, J., Somerville, C., Stitt, M., Torii, K.U., Waese, J., Wagner, D., McCourt, P. New Phytol. doi: 10.1111/nph.13687. [Epub ahead of print] (2015)

-.Transcriptional control of tissue formation throughout root development. Moreno-Risueno, M.A., Sozzani, R., Yardımcı, G.G., Petricka, J.J., Vernoux, T., Blilou, I., Alonso, J., Winter, C.M., Ohler, U., Scheres, B., Benfey, P.N. Science. 350:426-430 (2015)

-.Plant Functional Genomics. Alonso JM, Stepanova AN. Editors. Methods Mol Biol. ISBN: 978-1-4939-2443-1 (2015).

-.CESA TRAFFICKING INHIBITOR inhibits cellulose deposition and interferes with the trafficking of cellulose synthase complexes and their associated proteins KORRIGAN1 and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN1. Worden, N., Wilkop, T.E., Esteve, V.E., Jeannotte, R., Lathe, R., Vernhettes, S., Weimer, B., Hicks, G., Alonso, J., Labavitch, J., Persson, S., Ehrhardt, D., Drakakaki, G. Plant Phys. 2: 381-393 (2015)

-.Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana. Fàbregas, N., Formosa-Jordan, P., Confraria, A., Siligato, R., Alonso, J.M., Swarup, R., Bennett, M.J., Mähönen, A.P., Caño-Delgado, A.I., Ibañes, M. PlosGenetics. 11: e1005183 (2015)

-.A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana. Hu, Q., Merchante, C., Stepanova, A.N., Alonso, J.M., Heber, S. Bioinformatics Research and Applications. 138-149 (2015)

-.REGULATOR OF BULB BIOGENESIS1 (RBB1) Is Involved in Vacuole Bulb Formation in Arabidopsis. Han, S.W., Alonso, J.M., Rojas-Pierce, M. PlosOne 10: e0125621 (2015)

(2014)  

-.The Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation. Catalá R, López-Cobollo R, Mar Castellano M, Angosto T, Alonso JM, Ecker JR, Salinas J. Plant Cell. 26:3326-42 (2014)

-. Systems analysis of auxin transport in the Arabidopsis root apex. Band LR1, Wells DM, Fozard JA, Ghetiu T, French AP, Pound MP, Wilson MH, Yu L, Li W, Hijazi HI, Oh J, Pearce SP, Perez-Amador MA, Yun J, Kramer E, AlonsoJM, Godin C, Vernoux T, Hodgman TC, Pridmore TP, Swarup R, King JR, Bennett MJ. Plant Cell. 26:862-875 (2014)

-.Arabidopsis transformation with large bacterial artificial chromosomes. Alonso JM, Stepanova AN. Methods Mol Biol. 1062:271-83 (2014)

-.Genetic aspects of auxin biosynthesis and its regulation. Brumos J, Alonso JM, Stepanova AN. Physiol Plant. 151:3-12 (2014)

(2013)  

-.A Recombineering-Based Gene Tagging System for Arabidopsis. Alonso JM, Stepanova AN. Methods Mol Biol. 1062:271-283 (2014)

-.Local auxin sources orient apical-basal axis in Arabidopsis embryos. Robert H.S., Grones P., Stepanova A.N., Robles L.M., Lokerse A.S., Alonso J.M., Weijers D., Friml J. Curr. Biol. 23:2506-2512 (2013)

-.Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity. Pietra S., Gustavsson A., Kiefer C., Kalmbach L., Hörstedt P., Ikeda Y., Stepanova A., Alonso JM, Grebe M. Nat Commu 15;4:2779 (2013)

-.Molecular Mechanisms of Ethylene-Auxin Interactions. Robles L, Stepanova A, Alonso J. Molecular Plant.doi:10.1093/mp/sst113 (2013)

-.Ethylene signaling: simple ligand, complex regulation. Merchante C, Alonso JM, Stepanova AN. Curr Opin Plant Biol. 16:554-60. (2013)

-.Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition. Kopycki J, Wieduwild E, Kohlschmidt J, Brandt W, Stepanova AN, Alonso JM, Pedras MS, Abel S, Grubb CD. Biochem. J. 450:37-46 (2013)

-.Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. Hill K, Mathews DE, Kim HJ, Street IH, Wildes SL, Chiang YH, Mason MG, Alonso JM, Ecker JR, Kieber JJ, Schaller GE. Plant Physiol. 162:212-224 (2013)  

(Prior to 2013)  

-.AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. Péret B, Swarup K, Ferguson A, Seth M, Yang Y, Dhondt S, James N, Casimiro I, Perry P, Syed A, Yang H, Reemmer J, Venison E, Howells C, Perez-Amador MA, Yun J, Alonso J, Beemster GT, Laplaze L, Murphy A, Bennett MJ, Nielsen E, Swarup R. Plant Cell. 2012 24:2874-85 (2012)

-. The Arabidopsis YUCCA1 flavin monooxygenase functions in the indole-3-pyruvic acid branch of auxin biosynthesis. Stepanova AN, Yun J, Robles LM, Novak O, He W, Guo H, Ljung K, Alonso JM. Plant Cell. 23:3961-3973 (2011)

-. A Small-Molecule Screen Identifies L-Kynurenine That Competitively Inhibits TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth. He W, Brumos J, Li H, Ji Y, Ke M, Gong X, Zeng Q, Li W, Zhang X, An F, Wen X, Li P, Xie D, Stepanova A, Alonso J, and Guo H. Plant Cell. 23: 3944-3960 (2011)

-. Bypassing transcription: a shortcut in cytokinin-auxin interactions. Stepanova AN, Alonso JM. Dev. Cell. 21:608-610 (2011)

-. A recombineering-based gene tagging system for Arabidopsis. Zhou R, Benavente LM, Stepanova AN and Alonso JM. Plant J.66:712-723 (2011).

-. Ethylene signaling and response: where different regulatory modules meet. Stepanova AN. and Alonso JM. Curr Opin Plant Biol. 12:548-55 (2009)

-. Ikeda Y, Men S, Fischer U., Stepanova AN, Alonso JM, Ljung K, and Grebe M. Local auxin biosynthesis modulates gradient-dependent planar polarity in Arabidopsis Nature Cell Biol. 11:731-738 (2009)

-. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Stepanova AN, Robertson-HoytJ, Yun J, Benavente LM, Xie D, Doležal K, Schlereth A, Jürgens G, and Alonso JM.  Cell. 133:177-191 (2008)

-. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. O’Malley RC, Alonso JM, Kim CJ, Leisse TJ, and & Ecker JR. Nature Protocols 2:2910-17 (2007)

-. Multilevel Interactions between Ethylene and Auxin in Arabidopsis Roots. Stepanova AN, Yun J, Likhacheva AV, Alonso JM. Plant Cell 19:2169-85 (2007)

-. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Alonso JM, Ecker JR. Nat. Rev. Genet. 7:524-536 (2006)

-. Molecular mechanisms of ethylene signaling in Arabidopsis. Larissa M. Benavente and Jose M. Alonso. Mol. BioSyst. 2:165-173 (2006)

-. A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Stepanova AN, Hoyt JM, Hamilton AA, Alonso JM. Plant Cell. 17:2230-42 (2005)

-. Ethylene signaling and response pathway: A unique signaling cascade with a multitude of inputs and outputs. Stepanova, A.N. and Alonso, J.M. Physiol. Plant. 123:195-206 (2005).

-. The Ethylene Signaling Pathway. Alonso, J.M and Stepanova, A.S. Science 306:1513-1515 (2004)

-. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis.  Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR. Dev. Cell 7:193-204 (2004)

-. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C.C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D.E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W.L., Berry , C.C., Ecker, J.R. Science 301:653-657 (2003)

-. Five components of the ethylene-response pathway identified in a screening for weak ethylene-insensitive mutants in Arabidopsis. Jose M. Alonso, Anna N. Stepanova, Roberto Solano, Ellen Wisman, Simone Ferrari, Frederick M. Ausubel and Joseph R. Ecker. PNAS 100:2992-2997 (2003).

-. “The Ethylene Pathway: A Paradigm for Plant Hormone Signaling and Interaction”. Jose M. Alonso and Joseph R. Ecker. Science’s STKE (2001). http://stke.sciencemag.org/cgi/content/full/sigtrans;2001/70/re1.

-. “Chromosome 1 of Arabidopsis thaliana”. Theologis et al. Nature 408:816-820 (2000).

-. “EIN2, a Bifunctional Transducer of Ethylene and Stress Responses in Arabidopsis”. Jose M. Alonso, Takashi Hirayama, Gregg Roman, Saeid Nourizadeh and Joseph R. Ecker. Science 284:2148-2152 (1999).

-. “RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease-Related Copper Transporter, Is Required for Ethylene Signaling in Arabidopsis”. Takashi Hirayama, Joseph J. Kieber, Noriko Hirayama, Mikhail Kogan, Plinio Guzman, Saeid Nourizadeh, Jose M. Alonso, William P. Dailey, Andrew Dancis, and Joseph R. Ecker. Cell 97:383-393 (1999).