Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.
Anna BehleMaximilian DietschLouis GoldschmidtWandana MurugathasLutz C BerwangerJonas BurmesterLun YaoDavid BrandtTobias BuscheJörn KalinowskiElton Paul HudsonOliver EbenhöhIlka M AxmannRainer MachnéPublished in: Nucleic acids research (2023)
In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5'/3' gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.
Keyphrases
- transcription factor
- genome wide identification
- poor prognosis
- circulating tumor
- cell proliferation
- escherichia coli
- genome wide
- cell free
- single molecule
- single cell
- gene expression
- dna methylation
- cell therapy
- dna binding
- signaling pathway
- public health
- long non coding rna
- stem cells
- rna seq
- electronic health record
- machine learning
- circulating tumor cells
- genome wide analysis
- bone marrow