Research areas

Almost all our food, feed, fuel and fiber ultimately derives from plants. Understanding the genetic and environmental factors modulating plant growth is thus of great importance. Plants growth ultimately depends on photosynthesis, the process during which light energy is harnessed for the synthesis of high energy reduced carbon compounds. In order to capture light, plants have evolved unique ways of building cells, tissues and organs, a highly diverse metabolism, and a life-long continuation of versatile growth and development. Given the central importance of light for growth, plants posses numerous photoreceptors enabling them to sense changes in the amount, quality (color), photoperiod and direction of light (Figure 1). Our main goal is to understand how light modulates plant growth and development in order to enable these sessile organisms to optimize their growth habit depending on the environmental conditions.

Molecular genetic studies in Arabidopsis have identified four photoreceptor families that are present in all higher plants. There are three classes of blue light sensors: cryptochromes, phototropins and members of the Zeitlupe family. In addition the phytochromes enable plants to sense red and far-red light (Figure 1). In Arabidopsis these families are composed of two cryptochromes (cry1 and cry2), two phototropins (phot1 and phot2), three Zeitlupe-like sensors (ZTL, FKF1 and LKP2) and five phytochromes (phyA-phyE). Given that we mostly study phytochrome and phototropin-mediated signal transduction those two photoreceptors are presented in more detail.

The phytochromes

Phytochromes are synthesized as Pr (red-light absorbing); upon light excitation (red light is most effective) they are photo-transformed into Pfr (FR light absorbing), which is the active conformer. Light activation of the phytochromes triggers their accumulation in the nucleus where they mediate large changes in light-regulated gene expression (Figure 2). FR light leads to the rapid conversion of Pfr back to Pr, upon prolonged dark-treatment Pfr will spontaneously convert back to the inactive Pr conformer.

Light-regulated gene expression is partly mediated by the conformation-specific interaction between phytochromes in their Pfr conformation and a family of bHLH class transcription factors known as PIFs (Phytochrome Interacting Factor). Photon capture by these photoreceptors induces a suite of developmental responses including seed germination, seedling de-etiolation, regulation of tropic growth, shade avoidance and the control of flowering time (Figures 1 and 3). Some light responses are specifically induced by a single phytochrome (for example only phyA can trigger the de-etiolation response under a dense canopy, Figure 4), but there are many examples where integration of signals emanating from multiple photoreceptors is required (e.g. multiple phytochromes regulate gene expression in response to red light).

Figure 3: shade avoidance response in Arabidopsis. Rosettes of Arabidopsis plants grown either in sun-mimicking or shade-mimicking light conditions. Note the elongated petioles and the pale green colour of the plant grown in the shade. The spectrum of sunlight (red) and of light under a dense canopy (green) is indicated below. Plants are particularly sensitive to the R/FR ratio, which is slightly above 1 in the sun and can drop as low as 0.1 under dense vegetational cover. The R/FR ratio has a direct impact of the phytochrome photo-equilibrium (Pfr/Ptot). Christian Fankhauser © Unil

Figure 4: The phytochrome A loss-of-function mutant (phyA) is blind to far-red light (FR). A wild type (WT) and a phyA mutant grown in monochromatic far-red light. Note that the phyA mutants look like the wild type grown in the dark (D) as shown on the left of the image for comparison. Monochromatic FR light mimics the light condition encountered under deep vegetational cover. Chrisitan Fankhauser © Unil

The phototropins

The phototropins control phototropism (Figure 5), leaf positioning, chloroplast movements and opening of stomata. This class of photoreceptors thus largely contribute to the optimization of photosynthesis. The phototropins are blue-light activated protein kinases composed of two light-sensing LOV domains and a carboxy-terminal protein kinase domain. Blue light liberates the kinase domain from the inhibitory action of the amino-terminus of the protein containing the photosensory LOV domains. While the initial molecular events triggered by blue light at the level of the photoreceptor are quite well understood, the subsequent steps in signal transduction are still poorly understood (e.g. what are the substrates of the light-activated phtotropins?). A limited number of phototropin signal transduction elements have currently been identified. Our laboratory has studied members of the PKS (Phytochrome Kinase Substrate) family which have been shown to interact with phot1 and are essential for normal phototropism.

Figure 5: phototropism in an Arabidopsis seedling. An Arabidopsis seedling is photographed at hourly intervals following irradiation with unilateral blue light (light direction is indicated with an arrow). Note that within 2 hours of unilateral blue light asymmetric growth in the hypocotyl elongation zone leads to phototropism. Christian Fankhauser © Unil

 Main research areas

We perform our research with the model plant Arabidopsis thaliana. We combine molecular genetics, genome-wide expression studies, cell biology, biochemistry and imaging of growth processes in Arabidopsis to address the following specific aims:

1. Identify the molecular determinants leading to the specificity of phyA. Unlike other phytochromes, phyA can mediate light responses under conditions where the vast majority of the phytochrome is in its inactive Pr state (Figure 4). This correlates with the unique ability of phyA to accumulate in the nucleus in far-red light (mimicking light under a dense canopy).
2. Determine the mechanisms by which the phytochromes control PIF-mediated growth responses. We mostly concentrate our attention on the role of PIF4 and PIF5 in the regulation of growth during the shade avoidance response (Figure 6). We study the mechanisms by which the phytochromes regulate PIF activity and search for PIF target genes.
   
   
   
    

Figure 6: A model for the regulation of shade avoidance by the phytochromes and PIF (Phytochrome Interacting Factor) bHLH-class transcription factors. Phytochromes are synthesized in their Pr conformation (PrB for phytochrome B in its Pr conformation). Upon light activation they are converted to their active Pfr conformation (PfrB for phytochrome B in its Pfr conformation), which accumulates in the nucleus. In sunlight characterized by a high R/FR ratio (see figure 3) the phytochromes are mostly in their Pfr conformation. Pfr specifically interacts with PIF transcription factors leading to their proteolytic degradation. In the shade, which leads to a reduction of the R/FR ratio, the phytochrome photo-equilibrium is pushed towards the Pr conformer. PrB no longer interacts with PIF transcription factors leading to their accumulation and transcription of shade marker genes. Christian Fankhauser © Unil

3. Uncover the mode of action of PKS (Phytochrome Kinase Substrate) proteins in the control hypocotyl growth orientation and other phototropin-mediated responses (e.g. leaf flattening and positioning). Proper positioning of the stem and leaves is of central importance for the plant in order to optimize photosynthetic light capture. PKS proteins are involved both in phytochrome and phototropin signalling and may thus allow us to understand how these two photoreceptors co-ordinately control this growth response. Phototropism requires asymmetric growth of the shaded and lit sides of the hypocotyl. An important goal is to understand how this light response ultimately leads to asymmetric distribution of the plant hormone auxin, which is required for directional growth. Interestingly PKS4 is specifically expressed in the hypocotyl elongation zone, which undergoes asymmetric elongation during tropic growth (Figure 7).

Figure 7: PKS4 is specifically expressed in the hypocotyl elongation zone. GUS staining of 4-day-old etiolated PKS4pro:GUS lines. This expression pattern is particularly interesting given that these are the cells undergoing asymmetric elongation during tropic growth responses. Note that pks4 mutants have phototropic defects. Christian Fankhauser © Unil