Lab is located in Madrid, Spain and it is hosted by Centro de Biotecnología y Genómica de Plantas UPM – INIA (CBGP)
We are a 'hybrid' laboratory that combines theory and experiments.
Our focus is to mechanistically understand the design principles of hormone signaling circuits in plants and how those shape plant architectures. To achieve this goals we travel forward and backward between predictive computer models and quantitative biology experiments
We routinely combine:
Multilevel computer model simulations
Synthetic biology experiments
Time lapse microscopy
Krzysztof Wabnik | Principal Investigator
Address for the corespondence:
Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38,
Puzuelo de Alarcón, Madrid 28223, Spain
Marco Marconi | Postdoc
Mario García Navarrete | PhD student
Sara Pérez García | Undergrad student
Cristina Prieto Navarro | Technician/Lab manager
Daniel Alique Garcia | Postgrad student
Plants provide a fascinating example how to build to rebuild. Because they cannot run or escape, plants evolved 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
How dynamic environmental cues would impact on such self-organization manifested by patterns of spatiotemporal
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.
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.
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.
Right: 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 engineered organisms. We are interested in designing and implementing orthogonal hormone crosstalk mechanisms to that already present in model plant Arabidopsis Thaliana. We identify several 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.
Cell polarity dynamics
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 components of oscillator and their 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 cell imaging.
Sun, L., Feraru, E., Feraru, M. I., Wabnik, K., & Kleine-Vehn, J. PIN-LIKES coordinate brassinosteroid signalling with nuclear auxin input in Arabidopsis thaliana; 2019 BioRxiv, 646489. https://doi.org/10.1101/646489
Waidmann, S., Ruiz Rosquete, M., Schöller, M., Sarkel, E., Lindner, H., LaRue, T., Petřík I, Dünser K, Martopawiro S, Sasidharan R, Novak O, Wabnik K & Dinneny JR & Kleine-Vehn, J. Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Nature Commun. 2019, 10(1), 3540. https://doi.org/10.1038/s41467-019-11483-4
Žádníková P*, Wabnik K*, Abuzeineh A, Gallemi M, Van Der Straeten D, Smith RS, Inzé S, Friml J , Prusinkiewicz P and Benková EA model of differential growth-guided apical hook formation in plants, The Plant Cell, 2016, Oct;28(10):2464-2477. *co-first
Łangowski L, Wabnik K, Li H, Vanneste S, Naramoto S, Tanaka H and Friml J. Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells. Cell Discovery 2, Article number: 16018 (2016).
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. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nat Commun. 2015; 6:8821.
Šimášková M, O'Brien JA, Khan M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen JM, 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. Cytokinin response factors regulate PIN-FORMED auxin transporters.
Nat Commun. 2015; 6:8717.
Cuesta C, Wabnik K, Benková E. Systems approaches to study root architecture dynamics. Front Plant Sci. 2013; 4:537
Wabnik K, Robert HS, Smith RS, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Curr Biology 2013 Dec 16; 23(24):2513-8. PMID: 24291090. In press coverage [link]
Tian H*, Wabnik K*, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, and Ding Z (2014) WOX5 and IAA17-dependent feedback circuit regulates auxin-driven patterning of the Arabidopsis root tip, Molecular Plant 7(2):277-89 *co-first
Kleine-Vehn J*, Wabnik K*, Martiniere A, Langowski L, Willig K, Naramoto S, Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, S WH, Runions J, Friml J (2011) Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Mol Syst Biol 7:540, (Featured Article)
Wabnik K*, Kleine-Vehn J*, Govaerts W, Friml J (2011) Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends Plant Sci 16: 468-475, (Editorial Choice) *equal contribution
Wabnik K, Govaerts W, Friml J, Kleine-Vehn J (2011) Feedback models for polarized auxin transport: an emerging trend. Mol Biosyst 7: 2352-2359
Wabnik K*, Kleine-Vehn J*, Balla J, Sauer M, Naramoto S, Reinohl V, Merks RM, Govaerts W, Friml J (2010) Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. Mol Syst Biol 6: 447,*equal contribution
Wabnik K, Hvidsten TR, Kedzierska A, Van Leene J, De Jaeger G, Beemster GT, Komorowski J, Kuiper MT (2009) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics 25: 322-330