Open Access Research article

Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus

Wiebke Schröder1, Jörg Bernhardt2, Gabriella Marincola16, Ludger Klein-Hitpass3, Alexander Herbig4, Guido Krupp5, Kay Nieselt4 and Christiane Wolz1*

Author Affiliations

1 Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Elfriede-Aulhorn-Strasse 6, 72076 Tübingen, Germany

2 Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Str. 15, Greifswald, Germany

3 Institut für Zellbiologie, Universitätsklinikum Essen, Virchowstraße 173, 45122 Essen, Germany

4 Centre for Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen, Germany

5 AmpTec GmbH, Königstraße 4A, 22767 Hamburg, Germany

6 Present address: Research Centre for Infectious Diseases ZINF, University of Wuerzburg, Josef Schneider Str.2/ D15, Wuerzburg, Germany

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BMC Genomics 2014, 15:291  doi:10.1186/1471-2164-15-291

Published: 16 April 2014

Abstract

Background

It has been shown previously that aminocoumarin antibiotics such as novobiocin lead to immediate downregulation of recA expression and thereby inhibit the SOS response, mutation frequency and recombination capacity in Staphylococcus aureus. Aminocoumarins function by inhibiting the ATPase activity of DNA gyrase subunit B with a severe impact on DNA supercoiling.

Results

Here, we have analysed the global impact of the DNA relaxing agent novobiocin on gene expression in S. aureus. Using a novobiocin-resistant mutant, it became evident that the change in recA expression is due to gyrase inhibition. Microarray analysis and northern blot hybridisation revealed that the expression levels of a distinct set of genes were increased (e.g., recF-gyrB-gyrA, the rib operon and the ure operon) or decreased (e.g., arlRS, recA, lukA, hlgC and fnbA) by novobiocin. The two-component ArlRS system was previously found to decrease the level of supercoiling in S. aureus. Thus, downregulation of arlRS might partially compensate for the relaxing effect of novobiocin. Global analysis and gene mapping of supercoiling-sensitive genes did not provide any indication that they are clustered in the genome. Promoter fusion assays confirmed that the responsiveness of a given gene is intrinsic to the promoter region but independent of the chromosomal location.

Conclusions

The results indicate that the molecular properties of a given promoter, rather than the chromosomal topology, dictate the responsiveness to changes in supercoiling in the pathogen Staphylococcus aureus.

Keywords:
Staphylococcus aureus; Supercoiling; Gyrase; arlR; Spacer; Aminocoumarins; Novobiocin; Microarray; Voronoi tree map