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The Zur regulon of Corynebacterium glutamicum ATCC 13032.

Schröder J, Jochmann N, Rodionov DA, Tauch A - BMC Genomics (2010)

Bottom Line: The expression data were combined with results from cross-genome comparisons of shared regulatory sites, revealing the presence of candidate Zur-binding sites in the mapped promoter regions of five transcription units encoding components of potential zinc ABC-type transporters (cg0041-cg0042/cg0043; cg2911-cg2912-cg2913), a putative secreted protein (cg0040), a putative oxidoreductase (cg0795), and a putative P-loop GTPase of the COG0523 protein family (cg0794).Enhanced transcript levels of the respective genes in C. glutamicum JS2502 were verified by real-time RT-PCR, and complementation of the mutant with a wild-type zur gene reversed the effect of differential gene expression.Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, D-33615 Bielefeld, Germany.

ABSTRACT

Background: Zinc is considered as an essential element for all living organisms, but it can be toxic at large concentrations. Bacteria therefore tightly regulate zinc metabolism. The Cg2502 protein of Corynebacterium glutamicum was a candidate to control zinc metabolism in this species, since it was classified as metalloregulator of the zinc uptake regulator (Zur) subgroup of the ferric uptake regulator (Fur) family of DNA-binding transcription regulators.

Results: The cg2502 (zur) gene was deleted in the chromosome of C. glutamicum ATCC 13032 by an allelic exchange procedure to generate the zur-deficient mutant C. glutamicum JS2502. Whole-genome DNA microarray hybridizations and real-time RT-PCR assays comparing the gene expression in C. glutamicum JS2502 with that of the wild-type strain detected 18 genes with enhanced expression in the zur mutant. The expression data were combined with results from cross-genome comparisons of shared regulatory sites, revealing the presence of candidate Zur-binding sites in the mapped promoter regions of five transcription units encoding components of potential zinc ABC-type transporters (cg0041-cg0042/cg0043; cg2911-cg2912-cg2913), a putative secreted protein (cg0040), a putative oxidoreductase (cg0795), and a putative P-loop GTPase of the COG0523 protein family (cg0794). Enhanced transcript levels of the respective genes in C. glutamicum JS2502 were verified by real-time RT-PCR, and complementation of the mutant with a wild-type zur gene reversed the effect of differential gene expression. The zinc-dependent expression of the putative cg0042 and cg2911 operons was detected in vivo with a gfp reporter system. Moreover, the zinc-dependent binding of purified Zur protein to double-stranded 40-mer oligonucleotides containing candidate Zur-binding sites was demonstrated in vitro by DNA band shift assays.

Conclusion: Whole-genome expression profiling and DNA band shift assays demonstrated that Zur directly represses in a zinc-dependent manner the expression of nine genes organized in five transcription units. Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum.

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Genomic organization of the znr-zur gene region in corynebacterial genomes and M. tuberculosis H37Rv. (A), Comparison of the znr-zur genome region. The respective gene regions were obtained from C. glutamicum ATCC 13032 (NC_006958), C. efficiens YS-314 (NC_004369), C. diphtheriae NCTC 13239 (NC_002935), C. aurimucosum DSM44827 (NC_012590), C. accolens ATCC 49725 (NZ_ACGD00000000), C. urealyticum DSM7109 (NC_010545), C. jeikeium K411 (NC_007164), C. kroppenstedtii DSM44385 (NC_012704), and M. tuberculosis H37Rv (NC_000962). Orthologous genes are specifically labeled. Please note that the gene regions of C. jeikeium and C. accolens are shown in reversed orientation. (B), The znr upstream region of C. glutamicum ATCC 13032. The mapped transcription start site (+1) and the deduced core promoter regions (- 35 and - 10) are marked in bold. A stretch of six thymine residues representing a potential up-element is boxed. A putative ribosome-binding site (RBS) is indicated, the GTG start codon of znr is underlined.
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Figure 2: Genomic organization of the znr-zur gene region in corynebacterial genomes and M. tuberculosis H37Rv. (A), Comparison of the znr-zur genome region. The respective gene regions were obtained from C. glutamicum ATCC 13032 (NC_006958), C. efficiens YS-314 (NC_004369), C. diphtheriae NCTC 13239 (NC_002935), C. aurimucosum DSM44827 (NC_012590), C. accolens ATCC 49725 (NZ_ACGD00000000), C. urealyticum DSM7109 (NC_010545), C. jeikeium K411 (NC_007164), C. kroppenstedtii DSM44385 (NC_012704), and M. tuberculosis H37Rv (NC_000962). Orthologous genes are specifically labeled. Please note that the gene regions of C. jeikeium and C. accolens are shown in reversed orientation. (B), The znr upstream region of C. glutamicum ATCC 13032. The mapped transcription start site (+1) and the deduced core promoter regions (- 35 and - 10) are marked in bold. A stretch of six thymine residues representing a potential up-element is boxed. A putative ribosome-binding site (RBS) is indicated, the GTG start codon of znr is underlined.

Mentions: According to comparative genomic analysis, the cg2502 (zur) gene of C. glutamicum ATCC 13032 is located in a conserved gene region in all hitherto sequenced corynebacterial genomes (Fig. 2A). In the genomes of C. glutamicum, C. efficiens, C. diphtheriae, C. aurimucosum, and C. accolens, all representing members of the main lineage of the genus Corynebacterium [24,25], the zur gene is located downstream of another regulatory gene (znr) encoding a putative metal-sensing transcription regulator of the SmtB/ArsR protein family [4,10]. In genomes of corynebacteria belonging to the C. jeikeium and C. kroppenstedtii branches, the overall location of the zur gene is also conserved, but an orthologue of znr is lacking in front of the zur coding region (Fig. 2A). Since the orthologous protein of Znr from M. tuberculosis H37Rv (Rv2358) is apparently involved in zinc-dependent transcriptional (auto)regulation of the rv2358-furB operon [26], the homologous znr-zur gene region of C. glutamicum ATCC 13032 may also encode the regulatory switches involved in controlling the zinc homeostasis in this organism.


The Zur regulon of Corynebacterium glutamicum ATCC 13032.

Schröder J, Jochmann N, Rodionov DA, Tauch A - BMC Genomics (2010)

Genomic organization of the znr-zur gene region in corynebacterial genomes and M. tuberculosis H37Rv. (A), Comparison of the znr-zur genome region. The respective gene regions were obtained from C. glutamicum ATCC 13032 (NC_006958), C. efficiens YS-314 (NC_004369), C. diphtheriae NCTC 13239 (NC_002935), C. aurimucosum DSM44827 (NC_012590), C. accolens ATCC 49725 (NZ_ACGD00000000), C. urealyticum DSM7109 (NC_010545), C. jeikeium K411 (NC_007164), C. kroppenstedtii DSM44385 (NC_012704), and M. tuberculosis H37Rv (NC_000962). Orthologous genes are specifically labeled. Please note that the gene regions of C. jeikeium and C. accolens are shown in reversed orientation. (B), The znr upstream region of C. glutamicum ATCC 13032. The mapped transcription start site (+1) and the deduced core promoter regions (- 35 and - 10) are marked in bold. A stretch of six thymine residues representing a potential up-element is boxed. A putative ribosome-binding site (RBS) is indicated, the GTG start codon of znr is underlined.
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Related In: Results  -  Collection

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Figure 2: Genomic organization of the znr-zur gene region in corynebacterial genomes and M. tuberculosis H37Rv. (A), Comparison of the znr-zur genome region. The respective gene regions were obtained from C. glutamicum ATCC 13032 (NC_006958), C. efficiens YS-314 (NC_004369), C. diphtheriae NCTC 13239 (NC_002935), C. aurimucosum DSM44827 (NC_012590), C. accolens ATCC 49725 (NZ_ACGD00000000), C. urealyticum DSM7109 (NC_010545), C. jeikeium K411 (NC_007164), C. kroppenstedtii DSM44385 (NC_012704), and M. tuberculosis H37Rv (NC_000962). Orthologous genes are specifically labeled. Please note that the gene regions of C. jeikeium and C. accolens are shown in reversed orientation. (B), The znr upstream region of C. glutamicum ATCC 13032. The mapped transcription start site (+1) and the deduced core promoter regions (- 35 and - 10) are marked in bold. A stretch of six thymine residues representing a potential up-element is boxed. A putative ribosome-binding site (RBS) is indicated, the GTG start codon of znr is underlined.
Mentions: According to comparative genomic analysis, the cg2502 (zur) gene of C. glutamicum ATCC 13032 is located in a conserved gene region in all hitherto sequenced corynebacterial genomes (Fig. 2A). In the genomes of C. glutamicum, C. efficiens, C. diphtheriae, C. aurimucosum, and C. accolens, all representing members of the main lineage of the genus Corynebacterium [24,25], the zur gene is located downstream of another regulatory gene (znr) encoding a putative metal-sensing transcription regulator of the SmtB/ArsR protein family [4,10]. In genomes of corynebacteria belonging to the C. jeikeium and C. kroppenstedtii branches, the overall location of the zur gene is also conserved, but an orthologue of znr is lacking in front of the zur coding region (Fig. 2A). Since the orthologous protein of Znr from M. tuberculosis H37Rv (Rv2358) is apparently involved in zinc-dependent transcriptional (auto)regulation of the rv2358-furB operon [26], the homologous znr-zur gene region of C. glutamicum ATCC 13032 may also encode the regulatory switches involved in controlling the zinc homeostasis in this organism.

Bottom Line: The expression data were combined with results from cross-genome comparisons of shared regulatory sites, revealing the presence of candidate Zur-binding sites in the mapped promoter regions of five transcription units encoding components of potential zinc ABC-type transporters (cg0041-cg0042/cg0043; cg2911-cg2912-cg2913), a putative secreted protein (cg0040), a putative oxidoreductase (cg0795), and a putative P-loop GTPase of the COG0523 protein family (cg0794).Enhanced transcript levels of the respective genes in C. glutamicum JS2502 were verified by real-time RT-PCR, and complementation of the mutant with a wild-type zur gene reversed the effect of differential gene expression.Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, D-33615 Bielefeld, Germany.

ABSTRACT

Background: Zinc is considered as an essential element for all living organisms, but it can be toxic at large concentrations. Bacteria therefore tightly regulate zinc metabolism. The Cg2502 protein of Corynebacterium glutamicum was a candidate to control zinc metabolism in this species, since it was classified as metalloregulator of the zinc uptake regulator (Zur) subgroup of the ferric uptake regulator (Fur) family of DNA-binding transcription regulators.

Results: The cg2502 (zur) gene was deleted in the chromosome of C. glutamicum ATCC 13032 by an allelic exchange procedure to generate the zur-deficient mutant C. glutamicum JS2502. Whole-genome DNA microarray hybridizations and real-time RT-PCR assays comparing the gene expression in C. glutamicum JS2502 with that of the wild-type strain detected 18 genes with enhanced expression in the zur mutant. The expression data were combined with results from cross-genome comparisons of shared regulatory sites, revealing the presence of candidate Zur-binding sites in the mapped promoter regions of five transcription units encoding components of potential zinc ABC-type transporters (cg0041-cg0042/cg0043; cg2911-cg2912-cg2913), a putative secreted protein (cg0040), a putative oxidoreductase (cg0795), and a putative P-loop GTPase of the COG0523 protein family (cg0794). Enhanced transcript levels of the respective genes in C. glutamicum JS2502 were verified by real-time RT-PCR, and complementation of the mutant with a wild-type zur gene reversed the effect of differential gene expression. The zinc-dependent expression of the putative cg0042 and cg2911 operons was detected in vivo with a gfp reporter system. Moreover, the zinc-dependent binding of purified Zur protein to double-stranded 40-mer oligonucleotides containing candidate Zur-binding sites was demonstrated in vitro by DNA band shift assays.

Conclusion: Whole-genome expression profiling and DNA band shift assays demonstrated that Zur directly represses in a zinc-dependent manner the expression of nine genes organized in five transcription units. Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum.

Show MeSH
Related in: MedlinePlus