SYNTHETIC BIOLOGY OF PLANT SIGNALING CIRCUITS
Lab Web Page: http://www.plantdynamicslab.com
- Alique García, Daniel - PhD Student
- Atienza Sanz, Sara - Technician
- Avdovic, Merisa - PhD Student
- Marconi, Marco - Postdoctoral Fellow
- Riera Begué, Ainhoa - Student
- Ruffino, Nicola - PhD Student
- Sánchez Muñoz, Ignacio - Student
Plants provide a fascinating example how to build to rebuild. Because they cannot run or escape, plants evolved the regenerative,de novoorganogenesis potential which is manifested through self-organization of cells and tissues. Coordinated patterning of plants requires responses to numerous growth substances, so called phytohormones. Among those small signaling molecules auxins play a remarkable role in coordinating plant architecture such as meristem size, flower and leaf positioning, root growth and plant response to environmental cues. Our lab seeks answers to following questions:
- How does individual plant cell contribute to the dynamic collective behavior of a plant tissue?
- How dynamic auxin cues communicated between adjacent cells provide a principal driving force for self-organized multicellular patterning?
- How dynamic environmental cues would impact on such self-organization manifested by patterns of spatio-temporal oscillations and cell polarity establishment?
To find answers to these intriguing questions, we use the combination of multilevel computer model simulations, synthetic biology experiments and microfluidics. Currently lab employs a number of projects that access design principles of patterning mechanisms in plants that includes organogenesis, hormone signal processing and cell polarity dynamics.
Figure 1. Modelling-Experimental platform for quantitative synthetic biology of plant signaling circuits.
Computer models of hormone signaling in plant development
We are developing multilevel computer models of plant patterning that address principles of self-organization of plant body. These computer models integrate transport of hormones across tissues, polarity establishment and cell growth. Model systems under study include early embryogenesis, organogenesis, leaf venation patterning, organ bending and root patterning among others. Our daily routine involves close collaborations with experimentalists in order to develop precise models that can faithfully guide experiments in the future.
Oscillators in developmental biology
Lateral roots (LRs) determine the plant root architecture and thus are critical for adaptation and survival. Lateral roots are initiated in an iterative process that require cyclic activity of genes. Our team aim to identify the core genetic module behind such oscillations in the activity of downstream regulators involved in LR initiation. For that purpose we run computer model simulations to predict which genetic circuit architectures assembled from hormone signalling components would provide robust oscillatory dynamics. Next, we utilize model predictions to guide design and reconstruction of most promising genetic circuits in yeast and furthermore we quantify circuit dynamics on the customized microfluidics platform. This innovative approach allows us to quantitatively study circuit dynamics in isolation and with great precision and tunability. Until know, we were able to identify and implement in vivo auxin signalling circuits that could oscillate with a given frequency that can be tuned with auxin closely reassembling observations in plants. We also aim to compare the architecture of putative oscillator driving LR initiation with a synthetic implementation of vertebrate segmentation clock mechanism.
Figure 2. In vivo implementation of genetic oscillations in auxin signalling circuit involved in LR initiation.
Synthetic hormone crosstalk
Synthetic biology provides means to rewrite genetic pathways and design novel tasks that can be accomplished by genetically engineered organisms. We are interested in designing and implementing orthogonal hormone crosstalk mechanisms to that already present in model plant Arabidopsis Thaliana. We identified various plant hormone sensors that are present in archaic organisms such as bacteria. With synthetic biology approach we turn such sensors into genetic regulators i.e. activators and repressors and wire them together in positive and negative feedback loops. This fully synthetic “hormone cross talker” pathways could steer the regulation of downstream target involved in patterning of plant architecture. Currently we test prototypes of such circuits in yeast with the ultimate aim to port them back into plants in order to engineer plant architecture with superb precision.
Dynamics of cell polarity
Cell polarity is one of key innovations in cellular organization and cell-to-cell communication that allowed multicellular organisms to conquer the earth. In flowering plants, elements of male gametophyte known as pollen tubes show dynamic polarized growth that oscillates with high frequencies. A putative mechanism for such oscillations has been proposed that involves plant Rop GTPases, actin and calcium signaling. Nevertheless, core component of oscillations and its dynamics remains elusive. Our lab is interested in finding a minimal mechanism that could account for such fast posttranscriptional oscillations leading to transiently polarized growth and whether such mechanisms could be tuned by environmental cues. To achieve this goal we attempt to design and construct a minimal synthetic polarity oscillator in yeast using known regulators of polarized growth in plants and study its dynamics through time lapse live cell imaging.
- Programa de Atracción de Talento. Ayudas destinadas a la atracción de talento investigador a la Comunidad de Madrid en centros de I+D 2018-2022
Marconi, M., Gallemi, M., Benkova, E., Wabnik, K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife 10, e72132. DOI: 10.7554/eLife.72132
Marconi, M., Wabnik, K. 2021. Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis. Frontiers in Plant Science 12, 2171. DOI: 10.3389/fpls.2021.746183
Pérez-García, S., García-Navarrete, M., Ruiz-Sanchis, D., Prieto-Navarro, C., Avdovic, M., Pucciariello, O., Wabnik, K. 2021. Synchronization of gene expression across eukaryotic communities through chemical rhythms. Nature Communications 12, 4017. DOI: 10.1038/s41467-021-24325-z
Perianez-Rodriguez, J., Rodriguez, M., Marconi, M., Bustillo-Avendaño, E., Wachsman, G., Sanchez-Corrionero, A., De Gernier, H., Cabrera, J., Perez-Garcia, P., Gude, I., Saez, A., Serrano-Ron, L., Beeckman, T., Benfey, P.N., Rodríguez-Patón, A., del Pozo, J.C., Wabnik, K., Moreno-Risueno, M.A. 2021. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis. Science Advances 7, eabd4722. DOI: 10.1126/sciadv.abd4722
Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A., Abualia, R., Antonielli, L., Montesinos, J.C., Zhang, Y., Tan, S., Cuesta, C., Artner, C., Bouguyon, E., Gojon, A., Friml, J., Gutiérrez, R.A., Wabnik, K., Benková, E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. The EMBO Journal e106862. DOI: 10.15252/embj.2020106862
Li, H., Wangenheim, D. von, Zhang, X., Tan, S., Darwish‐Miranda, N., Naramoto, S., Wabnik, K., Rycke, R.D., Kaufmann, W.A., Gütl, D., Tejos, R., Grones, P., Ke, M., Chen, X., Dettmer, J., Friml, J. 2020. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. DOI: 10.1111/nph.16887
Sun, L., Feraru, E., Feraru, M.I., Waidmann, S., Wang, W., Passaia, G., Wang, Z.-Y., Wabnik, K., Kleine-Vehn, J. 2020. PIN-LIKES Coordinate Brassinosteroid Signaling with Nuclear Auxin Input in Arabidopsis thaliana. Current Biology. DOI: 10.1016/j.cub.2020.02.002
Waidmann, S., Rosquete, M.R., Schöller, M., Sarkel, E., Lindner, H., LaRue, T., Petřík, I., Dünser, K., Martopawiro, S., Sasidharan, R., Novak, O., Wabnik, K., Dinneny, J.R., Kleine-Vehn, J. 2019. Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Nature Communications 10, 1–14. DOI: 10.1038/s41467-019-11483-4
Žádníková, P., Wabnik, K., Abuzeineh, A., Gallemi, M., Straeten, D.V.D., Smith, R.S., Inzé, D., Friml, J., Prusinkiewicz, P., Benková, E. 2016. A Model of Differential Growth-Guided Apical Hook Formation in Plants. The Plant Cell 28, 2464–2477. DOI: 10.1105/tpc.15.00569
Łangowski, Ł., Wabnik, K., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., Friml, J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery 2, 16018. DOI: 10.1038/celldisc.2016.18
Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., Xuan, W., Lucas, J., Vassileva, V., Kitakura, S., Marhavý, P., Wabnik, K., Geldner, N., Benková, E., Le, J., Fukaki, H., Grotewold, E., Li, C., Friml, J., Sack, F., Beeckman, T., Vanneste, S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications 6, 8821. DOI: 10.1038/ncomms9821
Šimášková, M., O’Brien, J.A., Khan, M., Van Noorden, G., Ötvös, K., Vieten, A., De Clercq, I., Van Haperen, J.M.A., Cuesta, C., Hoyerová, K., Vanneste, S., Marhavý, P., Wabnik, K., Van Breusegem, F., Nowack, M., Murphy, A., Friml, J., Weijers, D., Beeckman, T., Benková, E. 2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications 6, 8717. DOI: 10.1038/ncomms9717
Tian, H., Wabnik, K., Niu, T., Li, H., Yu, Q., Pollmann, S., Vanneste, S., Govaerts, W., Rolčík, J., Geisler, M., Friml, J., Ding, Z. 2014. WOX5–IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis. Molecular Plant 7, 277–289. DOI: 10.1093/mp/sst118
Cuesta, C., Wabnik, K., Benková, E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science 4, 537. DOI: 10.3389/fpls.2013.00537
Wabnik, K., Robert, H.S., Smith, R.S., Friml, J. 2013. Modeling Framework for the establishment of the Apical-Basal Embryonic Axis in Plants. Current Biology 23, 2513–2518. DOI: 10.1016/j.cub.2013.10.038
Kleine‐Vehn, J., Wabnik, K., Martinière, A., Łangowski, Ł., Willig, K., Naramoto, S., Leitner, J., Tanaka, H., Jakobs, S., Robert, S., Luschnig, C., Govaerts, W., Hell, S.W., Runions, J., Friml, J. 2011. Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology 7, 540. DOI: 10.1038/msb.2011.72
Wabnik, K., Kleine-Vehn, J., Govaerts, W., Friml, J. 2011. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science 16, 468–475. DOI: 10.1016/j.tplants.2011.05.002
Wabnik, K., Govaerts, W., Friml, J., Kleine-Vehn, J. 2011. Feedback models for polarized auxin transport: an emerging trend. Molecular BioSystems 7, 2352–2359. DOI: 10.1039/C1MB05109A
Wabnik, K., Kleine‐Vehn, J., Balla, J., Sauer, M., Naramoto, S., Reinöhl, V., Merks, R.M.H., Govaerts, W., Friml, J. 2010. Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. Molecular Systems Biology 6, 447. DOI: 10.1038/msb.2010.103
Wabnik, K., Hvidsten, T.R., Kedzierska, A., Van Leene, J., De Jaeger, G., Beemster, G.T.S., Komorowski, J., Kuiper, M.T.R. 2009. Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics 25, 322–330. DOI: 10.1093/bioinformatics/btn625