ppGpp-mediated Genome orchestration during emergence of seedlings from soil – GODESS

When Arabidopsis seedlings germinate in darkness beneath the soil, they undergo skotomorphogenesis. This highly specialized developmental process is essential to facilitate the emergence of the young plantlet from the earth. As soon as the seedling emerges into the light, a drastic developmental shift occurs, initiating photomorphogenic development, characterized by greening, chloroplast biogenesis and the establishment of photosynthesis in the shoot. These early developmental transitions are marked by spectacular changes in cellular metabolism, subcellular organization, and in the transcriptional states of both the nucleus and organelles. Our previous research, along with others, has shown that: 1) Seedling emergence depends on plastid gene expression (PGE), during skotomorphogenesis and at the onset of photosynthesis. 2) It is associated with global shifts in the architecture and activity of the nucleus and organelles. 3) The nucleotide messenger guanosine tetraphosphate (ppGpp) plays a role in regulating PGE and photosynthesis. Based on preliminary data, the GODESS project now aims to uncover how ppGpp orchestrates plastid and nuclear functions for Arabidopsis seedling emergence. Using a set-up mimicking adverse soil conditions, we will employ multi-scale phenotyping, as well as metabolic, transcriptional, and biochemical profiling of Arabidopsis mutant lines in which ppGpp metabolism is modified. Through this research, we aim to deepen our understanding of how plants adapt to unfavorable soil conditions to ensure successful emergence. In addition to advancing fundamental scientific knowledge, we anticipate that the insights gained from this project will contribute to the improvement of methods for enhancing seedling vigor and, consequently, the resilience of crop yields in the face of exacerbated soil compaction and flooding conditions caused by changing climates.