The role of transcription-coupled DNA supercoiling in the coordination of temporal gene expression.
Bioinformatics and Theoretical Biology
Final Report Abstract
In this project we have studied the effect of transcription-coupled DNA supercoiling (TCDS) on the regulatory system. The different project parts were aimed at different aspects of regulation and the interaction with classical regulatory mechanisms. TCDS is the intrinsic effect of torsional stress caused by the inertia of RNAP migrating through the DNA helix. The directionality of transcription causes an unsymmetric supercoiling gradient that can affect promoter melting up -and downstream differently. Therefore, TCDS is a candidate for transcriptional regulation of genes within a range of approximately 10 kb. In this project we could show, that supercoiling sensitivity of genes and orientation of genes is coupled to exploit TCDS effects in a regulatory manner. Hence, the gene arrangement and evolution of the chromosome is partially determined by torsional effects caused by transcription. On top of the local TCDS effects, the global average supercoiling is changing during growth stages. Here We could show, that at different growth stages specific supercoiling sensitive genes are activated and repressed matching the overall level of supercoiling. Hence, a global supercoiling level is tuning the TCDS effects by adding or subtracting DNA supercoiling at each promoter, thereby damping or enhancing local TCDS effects. Moreover, we were able to link the neighbourhood based TCDS regulatory system to the orthogonal transcriptional regulatory network (TRN). We were able to show that genes regulated by transcription factors spread their regulatory information to neighbouring genes via TCDS, thus creating another level or regulation. This level represents operon like linking of gene expression without rigid tandem gene arrangements, allowing a evolutionary flexible regulation with respect to chromosome architecture. Finally, we studied the underlying priciples of promoter activity at the sequence level and found a connection between spacer sequence composition and gene expression. Taken together, we were able to elucidate several aspects of TCDS regulation on various levels and opened new questions for future projects.
Publications
- Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes. Nucleic Acids Res. 2016
Sobetzko, P
(See online at https://doi.org/10.1093/nar/gkw007) - MoCloFlex: A Modular Yet Flexible Cloning System. Front Bioeng Biotechnol, 7:271. 2019
Klein, CA, Emde, L, Kuijpers, A, Sobetzko, P
(See online at https://doi.org/10.3389/fbioe.2019.00271)
