Mapping the IscR regulon sheds light on the regulation of iron homeostasis in Caulobacter

Front Microbiol. 2024 Sep 30:15:1463854. doi: 10.3389/fmicb.2024.1463854. eCollection 2024.

Abstract

The role of the iron-sulfur [Fe-S] cluster transcriptional regulator IscR in maintaining [Fe-S] homeostasis in bacteria is still poorly characterized in many groups. Caulobacter crescentus and other Alphaproteobacteria have a single operon encoding [Fe-S] cluster biosynthesis enzymes. We showed that the expression of this operon increases in iron starvation, but not in oxidative stress, and is controlled mainly by IscR. Transcriptome analysis comparing an iscR null mutant strain with the wild-type (wt) strain identified 94 differentially expressed genes (DEGs), with 47 upregulated and 47 downregulated genes in the ΔiscR mutant. We determined the IscR binding sites in conditions of sufficient or scarce iron by Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq), identifying two distinct putative DNA binding motifs. The estimated IscR regulon comprises 302 genes, and direct binding to several regulatory regions was shown by Electrophoresis Mobility Shift Assay (EMSA). The results showed that the IscR and Fur regulons partially overlap and that IscR represses the expression of the respiration regulator FixK, fine-tuning gene regulation in response to iron and redox balance.

Keywords: Caulobacter crescentus; Fur; IscR; gene regulation; iron–sulfur cluster.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This study was supported by São Paulo Research Foundation (FAPESP, grants 2021/10577–0 and 2022/06360–8), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq-Brasil, grant 311418/2021–0). HA, LS, and BP were supported by fellowships from FAPESP (2018/17309–8, 2020/10171–0 and 2022/00308–4 respectively), HA from CNPq-Brasil (142391/2018–2), NS and BP by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001.