Behle, Anna ORCID: 0000-0002-0244-0312, Dietsch, Maximilian ORCID: 0000-0001-6955-1298, Goldschmidt, Louis, Murugathas, Wandana, Berwanger, Lutz C., Burmester, Jonas ORCID: 0000-0002-7926-7183, Yao, Lun, Brandt, David ORCID: 0000-0002-8859-8646, Busche, Tobias, Kalinowski, Jorn, Hudson, Elton P., Ebenhoeh, Oliver, Axmann, Ilka M. and Machne, Rainer (2022). Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis. Nucleic Acids Res., 50 (22). S. 12790 - 12809. OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

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Abstract

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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Behle, AnnaUNSPECIFIEDorcid.org/0000-0002-0244-0312UNSPECIFIED
Dietsch, MaximilianUNSPECIFIEDorcid.org/0000-0001-6955-1298UNSPECIFIED
Goldschmidt, LouisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Murugathas, WandanaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Berwanger, Lutz C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Burmester, JonasUNSPECIFIEDorcid.org/0000-0002-7926-7183UNSPECIFIED
Yao, LunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Brandt, DavidUNSPECIFIEDorcid.org/0000-0002-8859-8646UNSPECIFIED
Busche, TobiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kalinowski, JornUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hudson, Elton P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ebenhoeh, OliverUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Axmann, Ilka M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Machne, RainerUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-678208
DOI: 10.1093/nar/gkac1132
Journal or Publication Title: Nucleic Acids Res.
Volume: 50
Number: 22
Page Range: S. 12790 - 12809
Date: 2022
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1362-4962
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
ESCHERICHIA-COLI PROMOTER; RNA-POLYMERASE; GENE-EXPRESSION; DNA GYRASE; SIGMA-FACTORS; SUPERCOILING SENSITIVITY; HOMEOSTATIC REGULATION; CIRCADIAN-RHYTHMS; BACTERIOPHAGE-MU; TRANSCRIPTIONMultiple languages
Biochemistry & Molecular BiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/67820

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