Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs

• Published in: Molecular microbiology 2018-03, Vol.107 (6), p.704-717
• Main Authors: Garber, Megan E., Rajeev, Lara, Kazakov, Alexey E., Trinh, Jessica, Masuno, Duy, Thompson, Mitchell G., Kaplan, Nurgul, Luk, Joyce, Novichkov, Pavel S., Mukhopadhyay, Aindrila
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - metabolism; BASIC BIOLOGICAL SCIENCES; Binding; Coordination compounds; Copper; Copper - metabolism; DNA, Bacterial - metabolism; Efflux; Gene expression; Gene Expression Regulation, Bacterial; Genes; Genomes; Heavy metals; Homeostasis; Metals; Molecular Chaperones - metabolism; Operon; Operons; Protein Binding; Proteins; Pseudomonas stutzeri - genetics; Pseudomonas stutzeri - metabolism; Regulatory proteins; Regulatory sequences; Signal Transduction; Signalling systems; Target recognition; Zinc; Zinc - metabolism
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.13909

Summary Bacterial response to metals can require complex regulation. We report an overlapping regulation for copper and zinc resistance genes in the denitrifying bacterium, Pseudomonas stutzeri RCH2, by three two‐component regulatory proteins CopR1, CopR2 and CzcR. We conducted genome‐wide evaluations to identify gene targets of two paralogous regulators, CopR1 and CopR2, annotated for copper signaling, and compared the results with the gene targets for CzcR, implicated in zinc signaling. We discovered that the CopRs and CzcR have largely common targets, and crossregulate a core set of P. stutzeri copper and zinc responsive genes. We established that this crossregulation is enabled by a conserved binding motif in the upstream regulatory regions of the target genes. The crossregulation is physiologically relevant as these regulators synergistically and antagonistically target multicopper oxidases, metal efflux and sequestration systems. CopR1 and CopR2 upregulate two cop operons encoding copper tolerance genes, while all three regulators downregulate a putative copper chaperone, Psest_1595. CzcR also upregulated the oprD gene and the CzcIABC Zn2+ efflux system, while CopR1 and CopR2 downregulated these genes. Our study suggests that crossregulation of copper and zinc homeostasis can be advantageous, and in P. stutzeri this is enabled by shared binding motifs for multiple response regulators. We report an overlapping regulation of copper and zinc resistance genes in the denitrifying bacterium, Pseudomonas stutzeri that involves three DNA binding proteins. Our study suggests the observed crossregulation of the metal response is physiologically relevant, and is enabled by nearly identical motifs upstream of the copper and zinc responsive genes that recruit the three regulatory proteins.