Deciphering the role of translation in temperature-controlled development

Ambient temperature has profound effects on almost all aspects of plant development, from the onset of seed germination and seedling establishment to flower and fruit production. Consequently, temperature also strongly impacts crop quality and yield. With the progression of climate change, plants in temperate regions are challenged by more frequent heat waves as well as an overall rise in ambient temperature. Gaining insight into a plant's response to temperature is thus vital to fully understand how climate change will affect plant growth and development in the future and may also indicate ways to mitigate negative effects of rising temperatures on crop production.
We recently used Ribosome Profiling (Ribo-seq) to quantify the effect of warm temperature on translation dynamics in the model plant Arabidopsis thaliana at a global level. This allowed us to identify transcripts that undergo enhanced translation at warmer temperature, for instance the PIF7 transcript that encodes a key player in plant temperature signalling. In addition, this approach also allowed us to identify sequences upstream of a transcript's main open reading frame (ORF) that undergo translation. Such upstream open reading frames (uORFs) have recently attracted attention in many biological systems. While their precise mechanism still remains poorly understood, uORFs were often found to act as control elements for translation of the main ORF. In plants, uORFs have been found in 24-30% of transcripts, but a function has only been identified for few of them, linked to the control of morphogenesis, metabolism and disease resistance.
In our Ribo-seq data, we identified multiple Arabidopsis uORFs whose translation changes in a temperature-dependent manner. This project will employ genetic and molecular biology approaches to reveal the functions of several candidate uORFs in plant development and abiotic stress responses, with a particular emphasis on temperature-sensitive processes. It will also tackle the question whether and how these uORFs affect gene function, using in vitro and in vivo biochemical assays. These candidate gene-focused approaches will be complemented by transcriptome-wide analysis of translation initiation, aiming to reveal precise dynamics of uORF translation across a range of ambient temperatures. Together, these approaches will provide a detailed view of the temperature-regulated uORF landscape and reveal novel functions of temperature-sensitive uORFs in Arabidopsis.