Bacterial Genome Expansion: Domesticating New Replicons and Rewiring RNA Networks

• Applicant: Professor Dr. Kai Papenfort
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 569039131

Uptake and domestication of foreign DNA are fundamental aspects of bacterial evolution. However, the regulatory and evolutionary mechanisms driving bacterial genome expansion through the acquisition of large secondary replicons are only incompletely understood. To close this gap, the DRAWN project will focus on members of the Vibrio family, which carry a bipartite genome containing two essential replicons: chromosome 1 (Chr1) and chromosome 1 (Chr2). Recent clinical isolates of V. cholerae have been found to carry a third, megasized secondary replicon called Chr3. Uptake of Chr3 in this system provides a unique opportunity to explore how primary and secondary replicons are maintained together and how they influence gene expression and collective phenotypes, such as quorum sensing, biofilm formation, and virulence gene expression. In preliminary experiments leading to this proposal, we discovered that Chr3 is fully stable in V. cholerae and encodes various functions enhancing stress response, phage defense, and the virulence. Furthermore, we found that small regulatory RNAs (sRNAs) play important roles in the adaptation of Chr3 resulting in complex RNA network rewiring through RNA duplex formation and novel RNA binding proteins. To further explore this system and to understand how large horizontally-acquired genetic elements are incorporated and domesticated at the molecular level, we will perform global genomic analysis, including ChIP-seq, RNA-seq, RIP-seq, RIL-seq. In addition, we will employ marker frequency analysis, live-cell fluorescence microscopy, genome engineering, and experimental evolution to study the consequences of horizontal gene transfer at the population and single-cell level. Ultimately, our research will uncover the mechanisms underlying the acquisition and domestication of large replicons on host gene regulation and phenotypic variability that are key for microbial evolution and the adaptation to fluctuating environmental conditions.

• DFG Programme: Research Grants
• International Connection: France
• Cooperation Partner: Privatdozentin Dr. Marie-Eve Kennedy-Val