Jose Alonso

Hormone signal integration, recombineering, translation regulation, ribosome footprinting

Research Interests

Our main interest is to understand the molecular circuits plants use to integrate environmental and developmental signals to produce specific responses. Towards this general goal we have been focusing on the identification of the molecular “signal integrators” or “logic gates” involved in the interaction between two plant hormones, ethylene and auxin, in the regulation of root growth. Using a multidisciplinary approach (genetics, molecular biology, genomics, metabolomics, cell biology, etc.), we have uncovered a complex multistep integration process with both spatial and temporal components. Our research has shown that ethylene activates the transcription of auxin biosynthetic genes in the root meristem (root tip) and then auxin is transported upwards to where it sensitizes the cells in the division zone enabling them to properly respond to ethylene. Our more recent findings suggest that translation regulation represents a key aspect of this “sensitizing” mechanism triggered by auxin. In addition, these studies have allowed us to decipher the first complete auxin biosynthetic pathway in plants and we continue to investigate the role of auxin biosynthesis in development. Finally, we combine our interests in basic biology with the development and implementation of new genetic technologies to accelerate discoveries in plant biology. Currently, we are working on three main areas, gene modification in a chromosomal context using recombineering approaches, high-resolution whole-genome analysis of translation using next-generation-sequencing (NGS) -enabled ribosome footprinting, and implementation of metabolic biosensors, specifically a FRET (Fluorescence Resonance Energy Transfer) -based tryptophan biosensor.

Courses Taught

GN835 Functional Genomics (spring), GN810 Advanced Molecular Genetics Technologies (spring, odd years)

Selected Publications 

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

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. (2015) 50 years of Arabidopsis research: highlights and future directions New Phytol. doi: 10.1111/nph.13687. [Epub ahead of print]

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. (2015) Transcriptional control of tissue formation throughout root development Science. 350:426-430

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

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. (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 Plant Phys. 2: 381-393

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. (2015) Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana. PlosGenetics 11: e1005183

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

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

Catalá, R., López-Cobollo, R., Mar Castellano, M., Angosto, T., Alonso, J.M., Ecker, J.R., Salinas, J. (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. Plant Cell 26:3326-42

Band, L.R., Wells, D.M., Fozard, J.A., Ghetiu, T., French, A.P., Pound, M.P., Wilson, M.H., Yu, L., Li, W., Hijazi, H.I., Oh, J., Pearce, S.P., Perez-Amador, M.A., Yun, J., Kramer, E., Alonso, J.M., Godin, C., Vernoux, T., Hodgman, T.C., Pridmore, T.P., Swarup, R., King, J.R., Bennett, M.J. (2014) Systems analysis of auxin transport in the Arabidopsis root apex. Plant Cell 26:862-875

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

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

Stepanova A.N., Yun J., Robles L.M., Novak O., He W., Guo H., Ljung K., Alonso J.M. (2011) The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis, Plant Cell. 23(11):3961-73.

He W., Brumos J., Li H., Ji Y., Ke M., Gong X., Zeng Q., Li W., Zhang X., An F., Wen X., Li P., Chu J., Sun X., Yan C., Yan N., Xie D.Y., Raikhel N., Yang Z., Stepanova A.N., Alonso J.M., Guo H. (2011) A Small-Molecule Screen Identifies L-Kynurenine as a Competitive Inhibitor of TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth in Arabidopsis. Plant Cell. 23(11):3944-60.

Zhou R., Benavente L.M., Stepanova A.N,. Alonso J.M. (2011) A recombineering-based gene tagging system for Arabidopsis. Plant J. 66(4):712-23.

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

Stepanova A.N.*, Robertson-Hoyt J.,* Yun J., Benavente L.M., Xie D., Dolezal K., Schlereth A., Jurgens G., and Alonso J.M. (2008) TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell. 133:177-191 (*equal contribution)

Stepanova A.N., Yun J., Likhacheva A.V., Alonso J.M. (2007) Multilevel Interactions between Ethylene and Auxin in Arabidopsis Roots. Plant Cell. 19: 2169-2185.

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

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. (2003) Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana. Science 301: 653-657.