Dynamics of the Sinorhizobium meliloti genome architecture during symbiotic differentiation – SymGeAr

The Sym-GeAr project is based on our ongoing research in the Rhizobium-legume symbiosis, which showed that in certain legumes the endosymbiotic rhizobia, called bacteroids, undergo a terminal differentiation program that produces elongated cells in which the genome is amplified, abnormally methylated and chromatin compaction increased. Moreover, our study of bacteroid differentiation in the Medicago-Sinorhizobium meliloti interaction revealed that host-derived NCR signals and individual S. meliloti genes play a crucial role in this differentiation program. Here, we propose to evaluate the implication of a higher-order regulation in the bacteroid differentiation, at the level of the whole genome of the endosymbionts. We will apply state-of-the-art approaches to describe the genome architecture and address the question if dynamic genome 3D organization and epigenetic regulation are crucial for bacteroid differentiation in S. meliloti. A genome architecture map of free-living S. meliloti and bacteroids will be constructed using Hi-C as well as ATAC-seq. The distribution of the chromosome and secondary replicons across the cell will be analyzed using FROS. DNA methylation-based epigenetic modifications will be examined with SMRT-seq. The functional implications of (epi-)genome reorganization will be evaluated by reverse genetics targeting regulators introducing DNA methylation marks as well as nucleoid associated proteins and condensin that determine genome architecture. Both partners of SymGeAr are working on the rhizobium symbiosis but approach it from different angles. Partner 1 focuses on the physiology and mechanisms of cellular differentiation, while Partner 2 has accumulated a strong expertise on genome analyses and uses extensively -omics approaches and bioinformatics.