Synthetic biology of plant signaling circuits

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Research Outline

Plants provide a fascinating example how to build to rebuild. Because they cannot run or escape, plants evolved regenerative, de novo organogenesis 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 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.

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> 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.

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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.

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> 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 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 live cell imaging.

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