Abstract
BackgroundThe Bacillus subtilis Zur transcription factor recognizes a specific DNA motif, the Zur box, to repress expression of genes in response to zinc availability. Although several Zur-regulated genes are well characterized, a genome-wide mapping of Zur-binding sites is needed to define further the set of genes directly regulated by this protein.ResultsUsing chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we reported the identification of 80 inter- and intragenic chromosomal sites bound by Zur. Seven Zur-binding regions constitute the Zur primary regulon while 35 newly identified targets were associated with a predicted Zur box. Using transcriptional fusions an intragenic Zur box was showed to promote a full Zur-mediated repression when placed within a promoter region. In addition, intragenic Zur boxes appeared to mediate a transcriptional cis-repressive effect (4- to 9-fold) but the function of Zur at these sites remains unclear. Zur binding to intragenic Zur boxes could prime an intricate mechanisms of regulation of the transcription elongation, possibly with other transcriptional factors. However, the disruption of zinc homeostasis in Δzur cells likely affects many cellular processes masking direct Zur-dependent effects. Finally, most Zur-binding sites were located near or within genes responsive to disulfide stress. These findings expand the potential Zur regulon and reveal unknown interconnections between zinc and redox homeostasis regulatory networks.ConclusionsOur findings considerably expand the potential Zur regulon, and reveal a new level of complexity in Zur binding to its targets via a Zur box motif and via a yet unknown mechanism that remains to be characterized.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0345-4) contains supplementary material, which is available to authorized users.
Highlights
The Bacillus subtilis Zur transcription factor recognizes a specific DNA motif, the Zur box, to repress expression of genes in response to zinc availability
In the Gram positive bacterium Bacillus subtilis, transcription of genes involved in zinc homeostasis is regulated by Zur, a metalloprotein that binds Zn(II) as corepressor [6,7,8,9]
C-terminally sequential peptide affinity (SPA)-tagged Zur is a functional regulator The B. subtilis chromosome was modified at the zur locus to express Zur fused at its C-terminus with the SPA tag (ZurSPA)
Summary
The Bacillus subtilis Zur transcription factor recognizes a specific DNA motif, the Zur box, to repress expression of genes in response to zinc availability. Prestel et al BMC Microbiology (2015) 15:13 plays an important protective role against oxidative stress damage [19] Both ZosA and ZnuACB zinc transporters are involved in the competence developmental process [20]. Zinc homeostasis is maintained in B. subtilis thanks to a zinc-inducible efflux pump CzcD important for growth in the presence of high concentration of Zn(II) [5,21]. Expression of this system is regulated at the transcriptional level by the metalloregulator CzrA [5]
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