venus flytrap


Dr. José M. Alonso - Professor


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.


Selected Publications (10 out of 87)

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 2013 Nov 15;4:2779. doi: 10.1038/ncomms3779

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 (In press).

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.