Graduate Students Mini-Symposium VII 2021


16:00 - Srikanth Subramanian
"Dynamic bridging explains sub-diffusive movement of chromosomal loci"

Chromosomal loci in bacterial cells show a robust sub-diffusive scaling of the mean square displacement MSD ~ t^0.4 under various growth conditions and antibiotic treatments. Recent experiments have also shown that DNA-bridging Nucleoid Associated Proteins (NAPs) play an important role in chromosome organisation and compaction. Here, using polymer simulations we investigate the role of DNA bridging in determining the dynamics of chromosomal loci. We find that bridging compacts the polymer and reproduces the sub-diffusive dynamics of monomers at timescales shorter than the bridge lifetime. Furthermore, the measured scaling exponent defines a relationship between chromosome compaction and bridge lifetime. Based on the observed mobility of chromosomal loci, we predict a lower bound on the average bridge lifetime of ~ 9 seconds. Finally, we show how bridging influences the average mesh size of the polymer, an experimentally measurable quantity.

16:30 - Michael Seidel
"The link between CdbA and chromosome organization and segregation"

The ubiquitous second messenger c-di-GMP regulates a wide variety of processes in bacteria that are typically related to changes in lifestyle. Interestingly, we recently reported a link between c-di-GMP and chromosome biology. Specifically, we found that the nucleoid-associated protein CdbA, a DNA binding ribbon-helix-helix protein, is essential, binds c-di-GMP and is important for chromosome organization and segregation.Most nucleoid-associated proteins are not essential; therefore, to understand why CdbA is essential, we identified suppressor mutants of the lethal CdbA-depletion phenotype. We demonstrate that CdbZ, a c-di-GMP binding PilZ domain protein, is the essential player during CdbA depletion. Furthermore, we identified CdbZ interaction partners using pull-down experiments. This revealed several PilZ-domain proteins that additionally contain an Hsp70 domain, suggesting a role of c-di-GMP in cellular stress responses. Currently, we investigate how these proteins are connected and link c-di-GMP to chromosome biology.

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