PhD student Varvara Dikaya has studied how plants adjust to cold by focussing on the protein PORCUPINE (photo: Nabila El Arbi).
Plants have developed versatile processes to react to cold temperatures. Varvara Dikaya studied PORCUPINE, a protein that is part of a hub regulating responses to environmental cues like cold. In her PhD thesis, she showed that there is not just a single link between PORCUPINE and cold signalling, but multiple intertwined passes that act simultaneously.
To acquire cold resistance, plants developed complicated temperature sensing and adaptation mechanisms. Much of the research done so far to study such temperature responses focuses on changes in gene expression and on molecules that ensure cold resistance, for example amino acids, sugars and other molecules that prevent freezing. Components of the splicing machinery like the PORCUPINE protein were not part of this picture for a long time.
“Splicing acts as a central hub controlling the information flow from DNA to RNA defining which proteins are synthesised from a certain gene,” explains Varvara Dikaya who is working in Markus Schmid’s group at the Department of Plant Physiology, Umeå University, which is part of Umeå Plant Science Centre.
“Only recently attention shifted towards splicing proteins that play a role in cold signalling. One of these proteins is PORCUPINE which is named after the spiky look of the shoot tip of its mutant. It was discovered because Arabidopsis plants with mutated porcupine gene are cold sensitive.”
A single gene can give rise to multiple proteins
Many processes affect how many RNA copies are synthesised from a certain gene and which protein information these copies contain. During splicing, some parts of the initial RNA copy are cut out, changing the resulting sequence and information of the mature RNA that is used as template for the protein synthesis. This way a single gene can give rise to multiple mature RNAs and consequently different proteins.
“Splicing is a ubiquitous process common for animals, plants and fungi,” says Varvara Dikaya. “For plants, splicing is especially important when responding to environmental cues like for example cold. Depending on the growth conditions, the mature RNA copies synthesised from one gene can drastically differ and cause a redirection in the developmental programs.”
Hundreds of proteins are involved in splicing. Together with a special RNA type, they form a biological machine, the spliceosome. The spliceosome contains a core unit of several proteins which are evolutionary conserved. PORCUPINE is one of these core proteins, but, unlike many of the other core proteins, its loss makes plants particularly sensitive to cold.
“It is quite common to see growth and development alterations or even lethal effects when one of the core splicing proteins is mutated,” continues Varvara Dikaya. “The PORCUPINE mutant appears normal under ambient temperature conditions but cannot develop properly in case of even a mild temperature drop. Already at 16 degrees, the mutant grows shorter roots with increased root hair density and much smaller rosettes than normal. This is very special.”
PORCUPINE protein is involved in multiple intertwined signalling pathways
Varvara Dikaya and her colleagues were wondering in which way the PORCUPINE protein regulates responses to cold and why its loss causes cold sensitivity. However, the answer was not easy. They found that the PORCUPINE protein is involved in multiple intertwined signalling pathways.
On the one hand, temperature directly regulated the amount of the PORCUPINE RNA copies in the cell. The colder it is, the more RNA copies of the PORCUPINE gene were produced, assuming that also more PORCUPINE protein was available for the spliceosome. On the other hand, the spliceosome is tightly connected to the machinery that synthesises RNA from DNA - timewise and also with respect to its location in the cell. When one of the processes is adjusted to dropping temperatures, the other is likely to be affected as well. PORCUPINE might just be one of the multiple core splicing proteins that are affected by a general adjustment at the spliceosome making it very difficult to identify PORCUPINE-specific responses.
The researchers also investigate which genes’ splicing is directly controlled by PORCUPINE in a temperature-dependent manner. They identified several genes and some of them were key genes regulating the temperature response in plants. Varvara Dikaya and her colleagues think that the misregulation of these genes at least partially caused the specific look of the porcupine mutant.
“If all mentioned processes are coordinated properly in time and space, plants successfully adapt to the temperature drop,” concludes Varvara Dikaya. “Our current findings show the complexity of the cold response in plants. It is important to understand all aspects and identify fundamental mechanisms that could be applied later on in a practical manner. Such knowledge will be essential to create more resilient plants capable of withstanding environmental challenges in the future, but it is still a long way to go.”
Depending on the current needs of the cell, the reassembling of the different exons and introns during the splicing process can be adjusted resulting in different mature RNA variants and consequently various proteins with different functions. This so-called alternative splicing adds an additional level of complexity but allows more flexibility to adjust to changing conditions. In plants, it is especially important in response to environmental cues like temperature changes.
The splicing process: when a gene is activated, the DNA is transcribed into RNA via the protein complex RNA polymerase. The resulting RNA copy or RNA transcript is then processed by the spliceosome that cuts out introns (regions that are not important for the protein synthesis) and joints the remaining exons (regions that contain protein information). Depending on the needs of the cell, different variants of the mature RNA are assembled by the spliceosome (illustration: Varvara Dikaya).About the public defence:
Varvara Dikaya, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, will defend her PhD thesis on Friday, 28th of February 2025. Faculty opponent will be Richard Immink from Wageningen University and Research Centre, the Netherlands. The thesis was supervised by Markus Schmid.
Title of the thesis: Broken Sm-ring: A quest to the source of the cold sensitivity of the A.thaliana SmE1 splicing mutant
Link to Varvara Dikaya’s PhD thesis
For more information, please contact:
Varvara Dikaya
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
Text: Varvara Dikaya & Anne Honsel