Molecular logic of the Zur-regulated zinc deprivation response in Bacillus subtilis

Abstract

Bacteria respond dynamically to the changes in zinc availability. Repression by the Bacillus subtilis transcription factor Zur requires Zn(II), which binds with negative cooperativity to two regulatory sites per dimer to form, sequentially, Zur2:Zn3 and Zur2:Zn4 forms of the repressor. Here we show that, as cells transition from zinc sufficiency to deficiency, operons regulated by Zur are derepressed in three distinct waves. The first includes the alternative RpmEB(L31*) and RpmGC(L33*) ribosomal proteins, which mobilize zinc from the ribosome, whereas the second includes the ZnuACB uptake system and the YciC metallochaperone. Finally, as zinc levels decrease further, the Zur2:Zn3 form loses Zn(II) leading to derepression of RpsNB(S14*) and FolE2, which allow continued ribosome assembly and folate synthesis, respectively. We infer that zinc mobilization from intracellular zinc stores takes priority over energy-dependent import, and our results link the biochemistry of zinc sensing by Zur to the molecular logic of the zinc deprivation response.

Metal homeostasis and resistance in bacteria

“…Consequently, regulation of gene expression is often not an all or none event, but rather is finely tuned across operons with metalloregulatory binding sites of varying affinity and responsiveness 90,91 . Analysis of the resulting graded response has provided insights into how the cell prioritizes its responses to the gradual decline in available Zn(II) and may provide insights into which processes fail first.…”

“…Analysis of the resulting graded response has provided insights into how the cell prioritizes its responses to the gradual decline in available Zn(II) and may provide insights into which processes fail first. In the case of B. subtilis , derepression of the Zur regulon occurs in three distinct stages upon Zn(II) starvation, and these stages are correlated with the sequential loading of Zn(II) into the sensing sites of the dimeric repressor (Figure 2) 90 . In the first stage, Zn(II) that is already present in the cell and associated with the L31 and L33 ribosomal proteins is mobilized by expression of the Zn(II)-independent paralogs L31* and L33* 90 .…”

Metallochaperones and metalloregulation in bacteria

“…NikR thus provides an exceptional illustration of the importance of metal coordination geometry as a key feature of cognate metal sensing by a metalloregulatory protein, that is reinforced by the prevailing intracellular metalmilieu. In addition, the presence of lower affinity Ni II suggests the possibility of a graded response to Ni II stress, as has been documented for Zur ( vide supra ) [143]. …”

“…Apo-Zur, for example, generally refers to a form with Zn II bound to the structural Cys 4 site with the primary and secondary (if present) metal sites empty, while Zn 2 and Zn 4 forms refer to distinct holoforms with Zn II bound to the primary compared with primary and secondary (third) sites respectively. The precise metallation status of the repressor appears to differentially impact the binding of Fur or Zur to different DNA operators, enabling a graded response to increasing degrees of cellular metal limitation [143,144]. …”

A Novel Antimicrobial Approach Based on the Inhibition of Zinc Uptake in Salmonella Enterica

“…In contrast, when intracellular zinc levels are not sufficient to ensure its complete metallation, Zur loses its affinity for its target DNA sequences, thereby allowing expression of the controlled genes. Interestingly, zinT and znuA are transcriptionally activated at different zinc concentrations [16], suggesting that subtle differences in the Zur-binding sites reflect a hierarchical role of Zur-regulated genes in the response to zinc starvation, useful to establish a dynamic response to changes in zinc availability [18,19]. Despite the expression of zupT increases under condition of zinc deficiency, this gene is not regulated by Zur even though a putative Zur-binding site sequence has been identified in its promoter [13].…”