Dr. Kasper van Gelderen Light Signaling and Cell Biology
We investigate cell-biological aspects of plant light signaling; How photoreceptor complexes are organized in the nucleus and how the plant shoot can send signals to the root via mobile transcription factors.
Plant light perception through phytochromes
Plants need light to grow, so it makes a lot of sense that they can perceive the quantity and quality of light. To sense the shade of neighbouring plants, daylength, and even temperature and salinity, plants use the phytochrome photoreceptors. These receptors can be found in every cell of the plant and readout the amount of red and far-red light in the environment, which the plant uses as a cue for light quality. Phytochromes control a vast network of transcription factors that control, growth, allowing the plant top respond to the environment.
Nuclear condensates and liquid phase separation
Phytochromes can be found throughout the tree of life where organisms use them to detect light. They are a dimeric protein with a pigment inside the structure absorbs the light, driving the structure into a new conformation, ready to initiate signalling events. In the plant nucleus, photoreceptors, including phytochromes, coalesce into large protein condensates, phase-separating away from the rest of the nucleoplasm. These subnuclear compartments without membranes are flexible structures that integrate light perception and signalling. They can form and dissolve depending on the light environment, which is why they are called photobodies (see movie on the left). We want to understand how these compartment form, what they are made of, and how they function, in response to light.
HY5 shoot-root signaling
Light perception in the shoot by phytochromes also affects root development through mobile signals. Plants need to balance shoot and root development with regard to available light and nutrients. We investigate how HY5, a key transcription factor, is transported from shoot to root, communicating over long distance.
Research - Background & Approach: Cell Biology of Light Signaling
We are studying how light perception and light signalling is spatially integrated within the nucleus, cells and tissues of plants. Plant photoreceptors can be found in almost all of the cells of the plant body, and within these cells, they cluster into subnuclear phase separated compartments, which are large protein bodies that help concentrate, aggregate and regulate the factors that determine how the plant reacts to light, temperature and other environmental factors. Furthermore, we study how the root can react to the shoot-perceived light perceived by the action of shoot-to-root mobile transcription factors.
In our studies we use various imaging techniques such as confocal (live) imaging, super-resolution light microscopy, transmission electron microscopy and cry-electron tomography. We complement this with molecular biology, biochemistry and protein structure modelling techniques to study protein-protein interactions. To study the effects of light signalling, besides standard molecular genetics techniques, we use single nucleus transcriptomics and mathematical modelling, to unravel tissue and cell-specific aspects. This interdisciplinary approach helps us to understand how light receptor complexes function within tissues and at the structural level.
Phytochrome photobody formation and function
Phytochrome photobody formation and function
Phytochromes are the main red light sensors in plants and phytochromes form small (~500nm) subnuclear bodies, which also contain supporting cofactors and downstream transcription factors. These subnuclear structures are called photobodies and they play an important role in regulating light responses. Importantly, phytochrome B (phyB) is not only required for light-, but also for temperature-sensing, suggesting that photobodies also play an important role for plant responses to ambient temperature. Despite their importance, it remains unclear how the formation of photobodies aids phytochrome signaling, how output specificity is achieved in response to divergent stimuli and how this information influences plant developmental decisions. The formation of nuclear bodies is a general process in the eukaryotic nucleus, and lessons learned from photobodies may help us understand nuclear organization in general. To tackle these fundamental questions we investigate the formation and responses of photobodies to light and temperature using an integrated approach of high resolution live imaging and biochemistry. Using LEDs we create a dynamic light environment at the confocal microscope to create time-lapse images of nuclei, such as the movie depicted here (use the movie from the main page). Furthermore, we are employing proximity labelling to discover the composition of photobodies and chemical imaging screens to find new photobody-manipulating drugs. This project is funded by the DFG Emmy Noether programme
In addition, we are investigating what commonalities there are between photobodies by looking at a photobody-localizing protein and crucial light response factor, CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1). COP1 was one of the first plant proteins to have been observed in nuclear phase separated bodies and has been heavily studied over the years, with many functions being uncovered in regulating the plant light response. However, there is comparatively little study on how COP1 localizes to photobodies, and how that relates to phytochromes. By using similar techniques as described for phyB photobodies, we aim to uncover the role of COP1 in forming and maintaining photobodies. This project is funded by a DAAD-India fellowship
HY5 shoot-to-root transport
HY5 shoot-to-root transport
Plants can see competitors through the reflection of Far-Red light from neighbouring plant leaves, which helps them to avoid future competition for light; their sole energy source. A decrease in the red:far-red light ratio is perceived by phytochrome photoreceptors and leads to elongation responses above-ground. However, low red:far-red detection by the shoot also prompts plants to reduce their root growth, possibly to conserve resources. An important regulator in this response if the transcription factor, ELONGATED HYPOCOTYL 5 (HY5), which can be transported from the shoot to the root. There it has the ability to suppress auxin signaling and lateral root outgrowth. However, the mechanics of HY5 transport are not yet well understood and it is not clear whether the transport of HY5 is the direct link between shoot detected far-red light and a decrease in lateral root outgrowth.
Therefore, we study the mechanics and speed of HY5 transport, using confocal microscopy and HY5 inducible lines. We have constructed shoot-specific inducible lines to perform live-imaging of this transport with a vertical confocal microscope. With this setup we are able to follow the transport and unloading of HY5 from the phloem into the phloem pole pericycle, where it enters the nucleus. The question we are tackling now is how the shoot-borne HY5 is different from the root-borne HY5. Besides the aforementioned microscopy we are also employing micrografting, detailed phenotyping, proximity labelling and single nucleus sequencing. The project is funded by a DFG Walter Benjamin grant and a DAAD-Pakistan fellowship.
