From cold acclimation to thermomorphogenesis: a phosphoproteomics approach to decipher acclimation across the temperature spectrum

Climate change is leading to more irregular weather patterns, such as heat waves and cold spells, which negatively affect ecosystems and agriculture. The resulting temperature extremes cause a decrease in crop yields while global food demand continues to rise, threatening food security. Developing crops that can withstand temperature stresses is therefore crucial. Plants can adapt to temperature changes through processes called "acclimation," including cold acclimation to low temperatures and thermomorphogenesis for warm temperatures. One important mechanism of temperature acclimation is protein phosphorylation, where proteins are modified by adding or removing phosphate groups, thereby affecting their activity and stability. This process, regulated by kinases and phosphatases, is crucial for rapid cellular responses to fluctuating temperatures. This thesis explores the role of protein phosphorylation in plant temperature acclimation and identifies proteins that regulate both cold acclimation and thermomorphogenesis in plants. Chapter 1 reviews the importance of studying protein phosphorylation in temperature acclimation and the need to treat temperature as a continuous rather than binary signal. The chapter discusses existing research on regulators of both cold acclimation and thermomorphogenesis, such as protein kinases with temperature-specific phosphorylation targets. Chapter 2 presents a "thermal gradient table", equipment developed to expose plants to a range of temperatures in one experiment. The chapter demonstrates that plants show the expected traits associated with cold acclimation and thermomorphogenesis. In Chapter 3, phosphoproteomics is utilized to identify proteins whose phosphorylation status changes under different temperature conditions. The study shows that ABA-INDUCED EXPRESSION 1 (AIN1/PLATZ1) is differentially phosphorylated on serine (S)168 upon temperature changes. Platz1 showed enhanced hypocotyl elongation in high temperatures, while seedlings overexpressing PLATZ1 show the opposite phenotype. This suggests that PLATZ1 is a negative regulator of thermomorphogenesis and its role likely depends on (de)phosphorylation at high temperatures. Chapter 4 identifies INDUCER OF CBF EXPRESSION 1 (ICE1), a key regulator of cold acclimation, as a positive regulator of thermomorphogenesis. The ICE1 protein was more abundant in high temperatures and differentially phosphorylated on three different sites. Two of these sites are known to be essential for protein stabilization at low temperatures. Mutants of ice1 are less able to respond to high temperatures. We conclude that ICE1 regulates plant acclimation across the temperature spectrum, from low to high temperatures. In Chapter 5, the role of MITOGEN-ACTIVATED PROTIEN KINASE 6 (MPK6), a kinase known to negatively regulate cold acclimation, is examined in high-temperature responses. The study shows that MPK6 is also involved in thermomorphogenesis, acting as a negative regulator of hypocotyl elongation in response to high temperatures. Further research investigates MPK6 homologs in tomato and lettuce, finding that MPK1, the MPK6 homolog in these crops, plays a positive role in high-temperature growth, contrasting with its function in Arabidopsis. Finally, chapter 6 discusses the findings and their implications. The thesis identifies common regulators of both cold acclimation and thermomorphogenesis and develops a method to study temperature responses across a gradient. These insights and methodologies could contribute to the development of crops with enhanced temperature tolerance, aiding in future agricultural resilience to climate change.