Genome-wide mapping of nucleotide excision repair in arabidopsis root and shoot & the fate of LYM1/2 proteins during nodulation in Medicago truncatula

Plants, unlike many other organisms, are not mobile, which makes them vulnerable to a variety of hazardous factors such as ultraviolet (UV) light. UV light is known to cause DNA damage, which in turn leads to genetic instability. Organisms have found ways to cope with DNA damage by different molecular mechanisms to preserve genetic information flow properly. Nucleotide excision repair (NER) is a conserved mechanism widely utilized by many organisms, including plants. In this study, The Excision Repair Sequencing (XR-seq) method has been applied to shoot, root, and seedling tissues in Arabidopsis thaliana to map genome-wide DNA damage types: CPD and (6-4) PP. Arabidopsis thaliana has been shown to have transcription-coupled repair (TCR) in addition to global genome repair (GG-NER). Interestingly, root tissue, despite not being exposed to UV light, has demonstrated a significant amount of nucleotide excision repair, whose levels are similar to tissues exposed to UV. Root tissue might exhibit such repair due to the chemicals in soil, which might give rise to the formation of various DNA damage products repaired by the NER mechanism. Together with this finding, the repair dynamics could be further investigated in the model organism Arabidopsis to understand better essential players of DNA damage, gene activity, and chromatin accessibility throughout the plant genome. Medicago truncatula is a model legume that undergoes a mutualistic relationship with rhizobia under nitrogen-limited conditions to obtain ammonium (NH3). In this interaction, rhizobia produce ammonium from atmospheric nitrogen (N2) and provide it to the plant and in return, use the carbon source supplied by the plants. However, the question and mechanism of how the bacteria are allowed to maintain their cellular processes inside nodule organs within the root tissue of plants remain to be addressed in great detail. Lysin motif-containing receptor (LysM) proteins, LYM1 and LYM2, reside on plants' plasma membranes and are responsible for triggering innate immunity in response to patterns of bacterial peptidoglycan structures. Furthermore, upon arrival of rhizobia, the GPI anchors of LYM1 and LYM2 proteins are known to be cleaved that releases these proteins from symbiosome membrane. Thus, these proteins are inactivated to initiate an immune response so the intracellular rhizobia could survive, and the symbiotic relationship can be attained. This study includes cloning of LYM1 and LYM2 genes into plant expression vectors and genotyping lym1 and lym2 mutants. The questions of what the other interacting partners of LYM proteins are and what happens to LYM proteins in the absence of DNF2 protein need to be resolved in further studies.