Shedding light on nature's secrets
Just like human beings, plants are complex systems which respond to changes in their environment by initiating different processes and types of behaviour. And light is arguably the most important environmental factor for plants, providing energy for photosynthesis and affecting basic features such as architecture, flowering time and seed ripening/germination, plus a range of metabolic pathways. …
Scientists are now beginning to understand enough about the complex webs of genes responsible for this response to light, and thus may soon be able to change the way plants grow and develop, or transplant these light-sensitive networks into other organisms…
Science often comes up with solutions in search of a problem. For example, if you could make yeast dependent on light for its growth by transplanting a number of genes from a plant and connecting them to the networks which regulate yeast growth, then you could stop it growing simply by switching the light off. So far, no-one has come up with any practical use for such a breakthrough, but such knowledge could have major implications for biology, medical science and agriculture in years to come.
For Professor Ferenc Nagy, who was recently appointed the SULSA Professor of Cell and System Biology in the Biological School of the University of Edinburgh, such scientific breakthroughs have been common throughout his career, ever since he started fusing protoplasts (cell wall free plant cells) in the 1970s in his native Hungary, where he received his PhD in genetics in 1981 at the Biological Research Centre in Szeged. From 1983 to 1988 he worked in New York, at the Laboratory of Plant Molecular Biology headed by Professor Chua Nam-Hai at the Rockefeller University, as part of a team that pioneered the use of transgenic technology for studying regulated expression of genes in plants.
All his early work in Hungary trained Nagy in the fundamentals of tissue culture, including regenerating plants from single cells or fusing two plant cells and then selecting out only those plants that contained a certain combination of desirable features – a process known as ‘somatic cell fusion.’ During his time in New York, he also used his experience in tissue culture techniques to select and regenerate transgenic plants that expressed genes not found naturally in plants. These genes included bacterial and viral genes – as well as the gene coding for the human growth hormone. Professor Chua and his fellow researchers had ‘high hopes’ for this totally new branch of science as a tool to understand and manipulate the molecular circuits that regulate the expression of genes. The experiments also paved the way for later breakthroughs, transferring and expressing novel genes in plants to change their whole metabolism – for example, making them easier to cultivate or more resistant to herbicides, as well as more productive in various ways, such as producing more sugar, starch or oil. At this time, plant biotechnology was only just coming of age, but several years later, as interest in agrotechnology gathered momentum, it stirred up a public debate about the pros and cons of growing genetically modified (GM) crops that continues to grab the headlines today.
For Nagy, however, such applications were not his main interest, and in 1988, he returned to Europe to begin his independent research career at the Friedrich Miescher Institute in Basel, Switzerland, “to improve understanding of the biological functions of small-GTP binding proteins.” At this time, he also started to develop an interest in the study of how light affects plant growth and development – what biologists call photomorphogenesis. In 1996, he moved back to Hungary, and since then has published a number of seminal papers describing novel molecular mechanisms and components involved in “mediating light-induced, photoreceptor phytochrome-controlled signalling in plants.”
Nagy explains that plants have about 24,000 genes, with about 3,000 of these involved in photomorphogenesis, responding to different aspects of light (i.e. wavelength, intensity, quality, duration and direction) to mediate changes in growth throughout the life cycle. To achieve this feat, plants have developed special photoreceptors which, after sensing light, send signals to the rest of the plant to determine when to germinate and flower and when to synthesise flavonoids, and how to form leaves and branches and reach different heights (architecture) – as well as how to be successful in the battle for growth and survival. For example, plants living on the forest floor or at the top of the tree canopy should have different ways of responding to light, to optimise photosynthesis or simply help them compete, because features like wavelength (colour) and the intensity of the incipient sunlight are totally different in different locations. If you moved a successful plant from the shade to the sunlight, it may no longer thrive, and vice versa, because its light signalling network had been adapted to particular conditions, thus making it unable to trigger specific responses.
For example, the model plant Arabidopsis thaliana may have more than a dozen different photoreceptors absorbing the blue/UVA and red/far-red part of the spectrum. These different photoreceptors signal using different mechanisms and have specific and partly overlapping physiological functions. A common molecular event in signalling mechanisms launched by these photoreceptors is the regulated degradation or stabilisation of proteins, and Nagy is particularly interested in understanding and identifying the processes that regulate the stability of photoreceptors acting in the red/far-red part of the spectrum. His major challenge, however, is to decode the complex interactions or ‘cross-talk’ between them to identify their own specific functions and characteristics – in other words, find out how they work so we can manipulate particular genes to achieve specific objectives, such as faster growth or the ability to grow in different (perhaps even hostile) conditions.
Plants are sessile organisms (fixed in one position), Nagy explains, and therefore they have to adapt their metabolism to the actual environment. They actively monitor their environment not only for changes in light quality and quantity but also for water and nutrient supply, and have developed special mechanisms to cope with pathogen attacks. For example, some genes send signals which ‘talk’ about light whilst others send signals that talk about water availability or concentration of salt in the soil. If we alter one process in a genetically modified plant, it may promote fast growth or make the plant bigger under certain conditions, but lead to other less desirable features or even have a fatal effect on the plant under different conditions; whereas in naturally-cultivated plants these pathways are flexible and constantly adjust to the ever-changing environment.
According to Nagy, if one gene mutates and changes behaviour, this has a knock-on effect on the others. “For the last four or five years,” he says, “we have begun to understand that plants are complex entities, and that there is not a single signal cascade, but lots of cross-talk. We are looking at plants as biological systems, rather than studying their individual components.”
One major consequence of this research is that the data generated is becoming increasingly complex to process, and scientists like Nagy are increasingly turning to the high-tech solutions offered by systems biology to speed up the search for more answers, building complex models and performing tests to find out more about the ‘critical parameters,’ to identify the most important genes and receptors involved in certain tasks.
Sunlight has visible and invisible parts, and plants respond like humans to the invisible UVB light. This part of the spectrum is known to be harmful to the majority of living organisms (e.g. skin cancer in humans and burning of leaves in plants), so for these organisms it is essential to develop some sort of defensive mechanism to protect themselves from the mutagenic effects of UV. However, despite decades of intensive research, scientists still debate how organisms sense UV irradiation. “We think there is a special receptor for UV light in plants, which acts somewhat similarly to those that are active in the visible part of the spectrum,” says Nagy. During the last few years, as well as hunting the elusive UVB sensor, scientists have also discovered that some of the building blocks of signalling cascades launched by UVB and by visible light irradiation are common. In addition, they have been able to show that the UVB-specific signalling cascades regulate expression of several hundred genes, and Nagy is seeking to identify the most critical ones for defending the plant from the harmful effects of exposure to the mutagenic UVB light.
Nagy, who is also Scientific Advisor and Vice-Director of the Plant Biology Institute in the Biological Research Centre of the Hungarian Academy of Sciences in Szeged, and Honorary Professor at the University of Freiburg in Germany, is also doing major research into chronobiology, to understand how plants – like human bodies – measure time by “isolating new mutants that provide novel information about the molecular composition of the plant’s endogenous timekeeper, the circadian clock.”
As Nagy’s work becomes more complex – for example, mathematical modelling of signalling networks controlled by the phytochrome – he has had to learn new scientific ‘tricks’ and use the toolbox of systems biology, and being part of SULSA provides an opportunity to collaborate with other researchers which he hopes will benefit all of them and lead to further breakthroughs in genetic engineering, not only for plants but for humans.