- Research article
- Open Access
The Zur regulon of Corynebacterium glutamicum ATCC 13032
© Schröder et al; licensee BioMed Central Ltd. 2010
- Received: 15 June 2009
- Accepted: 7 January 2010
- Published: 7 January 2010
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.
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.
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.
- CGXII Minimal Medium
- Zinc Uptake System
- Zinc Uptake Regulator
- Corynebacterial Genome
Corynebacterium glutamicum is a gram-positive soil bacterium that is well-established for the industrial production of several L-amino acids [1, 2]. The complete genome sequence of the type strain C. glutamicum ATCC 13032 is available , and it was screened by bioinformatic tools to predict the repertoire of DNA-binding transcription regulators in this organism [4, 5]. Transcription regulators represent key components in the control of bacterial gene expression and permit the cell to sense and respond to environmental changes . Amongst others, metal ion homeostasis in bacterial cells is tightly regulated by specific metal-sensing transcription regulators. These metalloregulatory proteins, in principle, sense the intracellular levels of specific metal ions by binding them to a metal binding site, which leads to conformational changes affecting the regulator's ability to bind operator sites in regulatory DNA regions . Prominent protein families of metalloregulators are DtxR , MerR , SmtB/ArsR , and Fur . The ferric uptake regulator Fur was originally described as iron-sensing repressor of genes involved in siderophore biosynthesis and iron transport in Escherichia coli [12, 13], but Fur also activates the expression of many genes by either direct or indirect mechanisms and can be regarded as global transcription regulator of iron homeostasis in E. coli . Numerous studies indicated a tremendous diversity in metal selectivity and biological function within the Fur protein family that can be divided into sensors of iron (Fur), manganese (Mur), nickel (Nur), and zinc (Zur) .
Zinc is considered an essential nutrient for all living organisms. As zinc can be toxic at large concentrations , zinc uptake, efflux, storage, and metabolism is in general tightly regulated in bacteria . During our work on reconstructing the transcriptional regulatory network of C. glutamicum [5, 17], we recognized the Cg2502 protein as candidate to control the zinc metabolism in this species, since it was classified as DNA-binding transcription regulator of the Fur family  and iron metabolism is under global control of the dual regulator Cg2103, a member of the DtxR protein family . In this study, comparative whole-genome DNA microarray hybridizations revealed a set of differentially expressed genes that are under transcriptional control by Cg2502 (now named Zur). Comparative genomic analysis of Zur regulons in actinobacteria detected candidate Zur-binding sites within the mapped promoter regions of potential target genes in C. glutamicum ATCC 13032. The DNA binding of Zur to these operator sites occurred in a zinc-dependent manner and was verified by DNA band shift assays, providing clear evidence that Zur is involved in zinc-dependent transcriptional regulation of gene expression in C. glutamicum ATCC 13032.
Annotation of the corynebacterial zinc uptake regulator Zur
Transcriptional organization of the znr-zur gene region in C. glutamicum
Computational identification of actinobacterial Zur regulons
Overall, a conserved core of the reconstructed Zur regulons includes one or multiple paralogues of the zinc ABC-type transporter ZnuACB and a putative P-loop GTPase of the COG0523 family , orthologues of the B. subtilis YciC protein . In Mycobacterium species, P. acnes, S. coelicolor, and L. xyli, the Zur regulon includes paralogues of various ribosomal proteins (RpmB, RpmG, RpmE, RpmF, RpmJ, RpsN, RpsR). These observations are in agreement with the previously described Zur-dependent regulation of ribosomal protein genes in M. tuberculosis and S. coelicolor [31–33]. The znr-zur operon is preceded by a candidate Zur-binding site only in two Mycobacterium species (Fig. 4A). The C. diphtheriae Zur regulon includes the candidate ABC-type metal transporter operon troA-sapD-DIP0439-DIP0440-DIP0441-DIP0442 and the cmrA gene encoding a surface-associated protein . Additional candidate Zur-binding sites were detected upstream of the adhA gene encoding zinc-dependent alcohol dehydrogenase in C. glutamicum  and adhA orthologues in C. accolens and C. diphtheriae (Fig. 4A).
Global gene expression profiling of the zur-mutant C. glutamicum JS2502
Differentially regulated Zur target genes preceded by candidate Zur-binding sites in C. glutamicum ATCC 13032.
Differential gene expression2
ABC-type Zn/Mn transporter, substrate-binding protein
ABC-type Zn/Mn transporter, permease subunit
ABC-type Zn/Mn transporter, ATPase subunit
P-loop GTPase of the COG0523 family
ABC-type Zn/Mn transporter, substrate-binding protein
ABC-type Zn/Mn transporter, ATPase subunit
ABC-type Zn/Mn transporter, permease subunit
Differentially expressed genes in the zur mutant C. glutamicum JS2502 detected by DNA microarray hybridization and lacking candidate Zur-binding sites.
Differential gene expression1
ABC-type transporter, permease subunit
cold-shock protein A
putative secreted protein
anion-specific porin precursor
putative secreted protein
putative Co2+/Zn2+/Cd2+ efflux transporter
ABC-type transporter, substrate-binding protein
secondary ammonium transporter
phosphotransferase system component
putative membrane protease subunit
DNA-3-methyladenine glycolase I
putative flavin-containing monooxygenase
Verification of differential gene expression and promoter mapping
To support the conclusion that Zur is involved in transcriptional regulation of the potential target genes, control assays with a complemented C. glutamicum zur mutant were performed, thereby measuring the differential gene expression by RT-PCR. For this purpose, the zur gene was amplified by PCR and cloned into the C. glutamicum expression vector pEC-XK99E, resulting in plasmid pEC-XK99E_zur (Table 3). First, the differential expression of potential Zur target genes in C. glutamicum JS2502 was verified by real-time RT-PCR assays. As expected, the mRNA levels of all genes were clearly enhanced in the zur mutant when compared with the wild-type strain (Table 1), with the exception of the adhA gene (data not shown). Additional RT-PCR assays with the complemented strain C. glutamicum JS2502 [pEC-XK99E_zur] showed that the expression of potential target genes was indistinguishable from that of the wild-type strain ATCC 13032 carrying the empty cloning vector pEC-XK99E (data not shown). These results clearly demonstrated that the observed deregulation of gene expression can be attributed to the defined deletion of the zur gene in C. glutamicum JS2502.
Verification of zinc-dependent expression of the putative cg0042 and cg2911 operons
Verification of predicted Zur binding sites by in vitro DNA band shift assays
The zur gene encoding a zinc uptake regulator is conserved in genomes of actinobacteria
In the present study, we have examined the regulatory role of the C. glutamicum Zur protein (Cg2502) in the direct transcriptional control of gene expression. Zur was classified by protein domain pattern analysis as member of the Zur subgroup of the Fur protein family . Fur proteins form a ubiquitous group of metal-responsive transcription regulators in many diverse bacterial lineages [14, 42–44]. Comparative genomics revealed the presence of more than one fur homologue in most members of the taxonomic class Actinobacteria whose genome sequences have been completely determined, indicating that a gene duplication event predated the appearance of the last common ancestor of the actinobacteria . A corresponding evolutionary model suggested that the resulting paralogues maintained the main biochemical properties of the ancestor regulator, but became specialized for coordinating different metal ions [45, 46], including iron (Fur), manganese (Mur), nickel (Nur), and zinc (Zur) . An apparent gene loss event occurred in the common ancestor of the corynebacteria, as Corynebacterium genomes do not contain the furA gene encoding a regulator for oxidative stress genes, but have the orthologous furB (zur) genes . Accordingly, the zur gene product of C. glutamicum belongs to the small set of 24 transcription regulators that were detected in all hitherto sequenced corynebacterial genomes [5, 19]. Moreover, synteny analyses revealed a conserved chromosomal region surrounding the zur gene in corynebacteria and other actinobacteria, including Mycobacterium, Nocardia and Rhodococcus species . In these species, the zur gene is located downstream of another regulatory gene encoding a putative metal-sensing transcription regulator of the SmtB/ArsR protein family [10, 45]. Both regulators might be involved in controlling the balanced expression of genes involved in zinc uptake and metabolism in some actinobacteria [26, 47]. In M. tuberculosis, the rv2358-furB operon is (auto)regulated by Rv2358  and functions as the regulatory interface between the control of zinc uptake and efflux . At low zinc concentrations, Rv2358 negatively regulates expression of the zitA gene for a zinc efflux system  and the transcription of furB, thereby enabling the expression of FurB-regulated genes, including genes for zinc uptake systems . At high zinc concentrations, Rv2358 does not bind to the operator site in front of the rv2358-furB operon and, as a consequence, zinc uptake is prevented by the regulatory action of FurB and an excess of zinc is pumped out of the cell. Since the genomic localization and the transcriptional organization of the znr-zur operon in C. glutamicum ATCC 13032 is similar to that of M. tuberculosis H37Rv, the regulatory role of Cg2500 (Znr) might be similar to that of Rv2358, i.e. both transcription regulators work together to optimally balance the zinc concentration in the C. glutamicum cell. To verify this conclusion, the target genes of Znr and its zinc-dependent interaction with the corresponding regulatory DNA sites have to be determined in C. glutamicum in future studies.
The set of genes differentially expressed in the zur-mutant C. glutamicum JS2502 partially overlaps with the ethanol stimulon of C. glutamicum
The combination of genome-wide transcriptional profiling by DNA microarray hybridization and in vitro DNA band shift assays clearly demonstrated that the C. glutamicum Zur protein negatively controls the expression of five transcription units with genes that are involved in the zinc metabolism in this species. A comparison of the transcriptomes of the zur-deficient mutant C. glutamicum JS2502 and the wild-type strain C. glutamicum ATCC 13032 revealed 18 genes with increased expression in the zur mutant JS2502. This gene set, representing the cellular response to zur-deficiency in C. glutamicum JS2502, partially overlaps with a stimulon detected recently in C. glutamicum ATCC 13032 cells grown with ethanol as the sole carbon and energy source . Growth of C. glutamicum ATCC 13032 on ethanol was characterized by enhanced expression levels of 36 genes when compared with acetate- and glucose-grown cultures. The set of differentially expressed genes detected in both genome-wide profiling studies include: (i) cg0040 to cg0043 and cg2911 to cg2913 encoding putative ABC-type uptake systems for zinc ions, (ii) cg3096 encoding acetaldehyde dehydrogenase and (iii) cg3195 encoding a putative flavoprotein. On the other hand, an enhanced expression of the Zur regulon members cg0794 and cg0795 was not deteced during growth of C. glutamicum on ethanol. The genes for the putative zinc uptake systems showed the largest increase of mRNA levels in ethanol-grown cells of C. glutamicum, which was explained by the higher demand of zinc due to its incorporation into the zinc-dependent alcohol dehydrogenase (AdhA) of C. glutamicum . A candidate Zur-binding site was detected by cross-genome comparisons in the upstream region of adhA (cg3107), but the purified Zur protein did not bind to a corresponding 40-mer DNA sequence in vitro. In addition, the adhA gene was not detected as differentially expressed in the zur-deficient mutant C. glutamicum JS2502. Therefore, our results did not provide any evidence that the candidate Zur-binding site is involved in transcriptional regulation of adhA gene expression. The integration of the detected regulatory interactions into the database CoryneRegNet [48, 49] revealed that the Zur regulon forms a separate module in the transcriptional gene regulatory network model of C. glutamicum and is thus not linked to the currently known network supercluster . Whether an additional carbon source-dependent control of the Zur regulon by any kind of coregulation or hierarchical interaction is established in C. glutamicum remains to be elucidated.
Physiological function of genes belonging to the Zur regulon of C. glutamicum
Since the metal ions sensed by members of the Fur protein family are considered, on the one hand, fundamental for bacterial growth and, on the other hand, toxic at elevated levels, a strict balance between metal ion uptake and efflux is essential for homeostasis . The target genes of the C. glutamicum Zur protein detected in this study include two putative ABC-type transport systems (Cg0041-Cg0043 and Cg2911-Cg2913), a putative secreted protein (Cg0040), a putative oxidoreductase (Cg0795), and a putative P-loop GTPase of the COG0523 family (Cg0794) that may specifically bind Zn2+ ions . We also showed that Zur binds to the predicted operator sequences located in the mapped promoter regions of the respective genes, which are therefore under direct negative transcriptional control. The deduced genetic organization of the cg0794-cg0795 intergenic region and the common transcriptional control of both genes via two Zur operator sites suggests a functional link between the respective proteins. Since some experimentally characterized members of the COG0523 protein family of P-loop GTPases are so-called metallochaperones, such as HypB from Methanocaldococcus jannaschii  and UreG from Helicobacter pylori , the C. glutamicum P-loop GTPase Cg0794 may also function (eventually in conjuction with the oxidoreductase Cg0795) as a zinc-specific metallochaperone/insertase to enable the in vivo assembly of zinc-containing proteins under environmental conditions of zinc deficiency. Furthermore, Cg0794 is similar to YciC, an abundant protein from B. subtilis postulated to function as a metallochaperone . Expression of yciC in B. subtilis occurs in a zinc-dependent manner that is exerted by the B. subtilis Zur orthologue . YciC-like proteins are often members of the Zur regulons in proteobacteria and firmicutes and may be involved in the specific binding and allocation of Zn2+ ions . The Cg2911 (ZnuA1) and Cg0041 (ZnuA2) proteins of C. glutamicum belong to the TroA superfamily of metal-binding proteins that are predicted to function as initial receptors in ABC-type transport systems of metal ions , supporting the view that both systems are involved in transport of divalent metal ions, such as Zn2+. The transcriptional regulation of genes encoding zinc uptake systems by Zur proteins seems to be common in actinobacteria, as the zur gene is located adjacent to znu operons in Arthrobacter, Leifsonia, Acidothermus, Nocardioides, Streptomyces, Thermobifida, and Rubrobacter species . Likewise, genes encoding zinc ABC-type transport systems are under transcriptional control by Zur in Streptococcus suis , Xanthomonas campestris  and Yersinia pestis .
The transcriptional regulation of znu operons was characterized during genome-wide analyses of zinc-responsive regulators in M. tuberculosis H37Rv and Streptomyces coelicolor A3(2) [31–33]. The genes regulated by ZurMtub encode three putative metal transporters, a group of ribosomal proteins and proteins belonging to the early secretory antigen target 6 (ESAT-6) cluster and the ESAT-6/CFP-10 (culture filtrate protein 10) family . Likewise, ZurScoe controls the expression of znuACB, located upstream of zur and encoding a zinc uptake transporter, and of genes for paralogous forms of ribosomal proteins that are devoid of zinc-binding motifs and can therefore replace, during zinc deficiency, their zinc-binding counterparts that can serve as zinc storage forms [32, 33]. Three DNA binding sites of ZurScoe were determined by DNase I footprinting analysis, revealing the 7-1-7 inverted repeat TGAAAATGATTTTCA as consensus sequence of potential operator sites . This consensus sequence is similar to the central region of the 10-1-10 inverted repeat (candidate Zur-binding site) detected in the C. glutamicum genome in the present study. Likewise, DNA protection assays were used to identify Zur binding sites in the M. tuberculosis genome sequence . The deduced 10-1-10 inverted repeat is also similar to the consensus sequence of Zur binding sites detected in the genome of C. glutamicum. Accordingly, the Zur binding sites in actinobacteria are apparently represented by a conserved 21-bp palindromic sequence with a 1-bp non-palindromic center, as shown by the Zur-binding motif sequence logo (Fig. 4B).
The combination of cross-genome comparison of shared regulatory sites and whole-genome expression profiling with DNA microarrays allowed us to deduce the Zur regulon of C. glutamicum ATCC 13032. It consists of five transcription units covering nine genes and encoding the components of two potential ZnuACB zinc transporters, a putative secreted protein, a putative oxidoreductase, and a putative P-loop GTPase of the COG0523 protein family. In vivo expression studies and in vitro DNA band shift assays demonstrated that Zur directly represses the expression of its target genes in a zinc-dependent manner. Accordingly, the Zur (Cg2502) protein is the key transcription regulator for genes involved in zinc homeostasis in C. glutamicum.
Bacterial strains, plasmids and growth conditions
Bacterial strains and plasmids used in this study.
Strain or plasmid
Source or reference
C. glutamicum ATCC 13032
C. glutamicum JS2502
ATCC 13032 with defined deletion in zur
E. coli DH5αMCR
E. coli strain used for standard cloning procedures
E. coli TOP10
E. coli strain used for cloning of RACE-PCR products
lacZα, Apr; E. coli cloning vector
sacB, Kmr; E. coli vector for allelic exchange
sacB, Kmr; pK18mobsacB carrying a modified zur gene with internal deletion
PTet, strep-tag, Apr; E. coli expression vector
pASK-IBA5+ carrying the C. glutamicum zur gene
gfpuv PL , Kmr; promoter-probe vector
gfpuvPL, Kmr; pEPR1 carrying the znr upstream region
gfpuvPL, Kmr; pEPR1 carrying the zur upstream region
gfpuvPL, Kmr; pEPR1 carrying the cg0042 upstream region
gfpuvPL, Kmr; pEPR1 carrying the cg2911 upstream region
P trc , lacI, Kmr; C. glutamicum expression vector
P trc , lacI, Kmr; pEC-XK99E vector carrying the zur gene for complementation
DNA preparation and PCR techniques
The preparation of plasmid DNA from E. coli cells was performed by the alkaline lysis technique using the QIAprep Spin Miniprep Kit (Qiagen). The protocol was modified for C. glutamicum cells by using 20 mg ml-1 lysozyme in resuspension buffer P1 and by incubating the assay at 37°C for 3 h. Chromosomal C. glutamicum DNA was isolated as described previously . DNA restriction, analysis by agarose gel electrophoresis and DNA ligation were performed according to standard procedures . The transformation of plasmid DNA was carried out by electroporation using electrocompetent E. coli and C. glutamicum cells [60, 61]. The DNA amplification by PCR was performed with a PTC-100 thermocycler (MJ Research) and BIOTAQ DNA polymerase (Bioline) or Phusion Hot Start High-Fidelity DNA polymerase (Finnzymes). The PCR products were purified with the PCR Purification Spin Kit (Qiagen). All Oligonucleotides used in this study were purchased from Operon Biotechnologies (see additional file 2).
Construction of a defined zur deletion in C. glutamicum
The gene SOEing procedure  was applied to establish a defined deletion of 195 nucleotides in the zur coding region. The PCR primers used for gene SOEing were cg2502 del1 to cg2502 del4 (see additional file 2). The resulting pK18mobsacB derivative, pK18mobsacB _Δzur (Table 3), was applied to perform an allelic exchange by homologous recombination in the chromosome of C. glutamicum ATCC 13032 , resulting in the mutant strain C. glutamicum JS2502. To complement the zur mutant phenotype, a DNA fragment covering the complete coding region of zur was amplified by PCR with the primer pair cg2502_ compl1 and cg2502_ compl2 (see additional file 2), digested with EcoRI and BamHI, and cloned in E. coli into the corresponding sites of shuttle expression vector pEC-XK99E (Table 3).
Testing in vivo promoter activity
The upstream region of the zur (cg2500) gene and the znr-zur intergenic region were amplified from chromosomal C. glutamicum DNA by PCR with the primer pairs cg2500 _GFP1-cg2500 _GFP2 and cg2502 _GFP1-cg2502 _GFP2, respectively (see additional file 2). The PCR products were digested with appropriate enzymes and cloned into compatibel sites of the promoter-probe vector pEPR1  that contains the promoterless gfp reporter gene coding for the green fluorescent protein. The reporter gene of pEPR1 will be expressed only if the DNA fragment cloned in front of gfp contains an active promoter . The expression of the gfp gene in E. coli DH5αMCR and C. glutamicum ATCC 13032 was detected by fluorescence microscopy with an Axiophot microscope (Zeiss) at a 400-fold magnification. All digital GFP pictures were taken with an exposure time of four seconds.
Measurement of in vivo promoter activity for cg0042 and cg2911
To detect a zinc-dependent expression of the cg0042 and cg2911 operons, approx. 200 bp segments covering the respective core promoter regions were amplified from chromosomal C. glutamicum DNA by PCR with the primer pairs cg0042 _GFP1-cg0042 _GFP2 and cg2911 _GFP1-cg2911 _GFP2, respectively (see additional file 2). The PCR products were cloned in E. coli DH5αMCR into the promoter-probe vector pEPR1, providing a promoterless gfp reporter gene for subsequent measurements . The plasmids were transformed into C. glutamicum ATCC 13032 and the zur mutant C. glutamicum JS2502 by electroporation. The resulting strains were grown in CGXII minimal medium containing 1 mg l-1 ZnSO4 (high Zn condition) and in CGXII without additional ZnSO4 (low Zn condition). Additionally, the cells were exposed to 10 μM of the chelator N,N,N',N'-tetrakis-(2-pyridylmethyl)-ethylenediamine (TPEN) for 3 h in CGXII minimal medium (Zn-chelated condition). Expression of the gfp reporter gene was measured by real-time RT-PCR using the primers LCPrimer1_gfp and LCPrimer2_gfp (see additional file 2).
RNA techniques and DNA microarray hybridizations
The isolation and purification of total RNA from C. glutamicum cells was carried out as described previously . The transcript levels of genes were measured by real-time reverse transcription PCR (RT-PCR) with the LightCycler instrument (Roche Applied Scince), using the SensiMix One-Step Kit (Quantace). The differences in gene expression between C. glutamicum JS2502 and the wild-type strain ATCC 13032 were determined by comparing the crossing points of two biological samples, each measured with two technical replicates. The measured crossing point (CP) is the cycle at which PCR amplification begins its exponential phase and is considered the point that is most reliably proportional to the initial RNA concentration (Roche Applied Science). The amounts of the mRNAs of the genes were normalized on total RNA, and the relative change in transcription rate was determined as 2-ΔCP, with ΔCP equal to the difference of the measured crossing points for the test and the control condition. The crossing points were calculated by the LightCycler software (Roche Applied Science). The quality of the measurement was ensured by melting curve analysis.
Transcription start sites were determined by using the 5'/3' RACE Kit second generation according to the manufacturer's instructions (Roche Applied Science). Starting with 1 μg of total C. glutamicum RNA, this approach enables the transcription of gene specific mRNA sequences into first-strand cDNA with the cDNA synthesis primer SP1 (see additional file 2). This initial cDNA synthesis was followed by a further amplification with nested PCR using the gene specific primer SP2 (see additional file 2). All PCR procedures were performed according to the recommendations of the manufacturer (Roche Applied Science) with a PTC-100 thermocycler (MJ Research). The PCR products were cloned into the pCR2.1-TOPO vector using the TOPO TA Cloning Kit (Invitrogen), and the resulting plasmids were transferred into chemically competent E. coli TOP10 cells. The cloned RACE-PCR products were finally sequenced to determine the 5' end of the mRNA (IIT Biotech).
For global transcription profiling, hybridization of whole-genome DNA microarrays was performed with total RNA probes isolated from two independently grown C. glutamicum cultures. The respective cDNA samples were labeled with Cy3/Cy5 in one experiment and with Cy5/Cy3 in the other one (label swapping). Since each C. glutamicum DNA microarray contains four spots per gene, a maximum of eight spots per gene provided data for calculating differential gene expression. To minimize the number of false-positive signals, hybridization data were stringently filtered to obtain genes with at least six statistically significant values out of the eight technical replicates, applying an error probability of less than 5% for the t-test . The data normalization was carried out with the LOWESS function, and t-test statistics were calculated with the EMMA2 software package . The microarray hybridization data were deposited in the CoryneRegNet database with identifier "delta_zur" and can be downloaded for further analysis by using SOAP-based web services .
Overexpression and purification of the C. glutamicum Zur protein
To fuse the C. glutamicum Zur protein with an amino-terminal streptavidin (strep)-tag, the coding region of the zur gene was amplified by PCR with the primer pair cg2502 _fwd_5Strep and cg2502 _rev_5Strep (see additional file 2), which were created by using the IBA Primer D'Signer1.1 software (IBA BioTAGnology). The resulting PCR product was digested with BsaI and cloned into pASK-IBA5+ to give plasmid pASK-IBA5+_cg2502 (Table 3) that was transferred to E. coli DH5α MCR. Cell culturing, overexpression of the recombinant Zur protein and purification with Strep-Tactin sepharose-packed columns were carried out according to the manufacturer's instructions. The RiboLyser instrument was used for cell disruption, with a speed rate of 6.5 for two time intervals of 30 s and ice-cooling of 1 min in-between. The concentration of the eluated protein was determined with the Bio-Rad protein assay kit (Bio-Rad Laboratories), and the eluate was analyzed by SDS-PAGE. To verify the purification of the Zur protein, an in-gel digestion with modified trypsin (Promega) was carried out. A peptide mass fingerprint of the purified protein was determined by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, applying an Ultraflex mass spectrometer (Bruker Daltonics) and the MASCOT software.
DNA band shift assays with streptavidin-tagged Zur protein
Purified Zur protein was used in electrophoretic mobility shift assays (EMSAs) to determine its ability to interact with in silico predicted operators in dependence on zinc. EMSAs were performed using fluorescein-labeled 40-mer oligonucleotides that were annealed with complementary oligonucleotides to double-stranded DNA fragments by heating for 5 min at 94°C and cooling on ice for 15 min. The binding assays were performed in a final volume of 20 μl, containing 0.05 pmol of the double-stranded 40-mer, 40 pmol of strep-tagged Zur protein, 0.06 μg herring sperm DNA, and binding buffer (20 mM Tris-HCl, 50 mM KCl, 1 mM DTT, 50 μg ml-1 bovine serum albumin, 5% glycerol; pH 8.0). EDTA was added to the binding reaction to a final concentration of 400 μM . Ions (ZnCl2, MgSO4, NiCl2, CuSO4, MnSO4, or FeSO4) were added to EMSAs in a concentration of 50 μM. The assays were incubated at 30°C for 30 min and separated in 2% agarose gels prepared in gel buffer (40 mM Tris-HCl, 10 mM sodium acetate, 1 mM EDTA; pH 7.8). A voltage of 70 V was applied for 1 h. The agarose gels were scanned with a Typhoon 8600 Variable Mode Imager (Amersham Biosciences Europe).
Bioinformatic methods and comparative genomic analysis of Zur regulons
The complete genomes of actinobacteria were downloaded from GenBank . The Actinobacteria-specific training set for the identification of the Zur-binding motif was composed of the candidate zinc transporter genes znuABC. The DNA motif search profiles (a positional-weight matrix) were constructed using the SignalX program. Analyzed genomes were scanned with the constructed Zur-binding motif profile using the Genome Explorer software , and the identified genes with candidate Zur-binding sites were analyzed by the consistency check comparative procedure as previously described . Positional nucleotide weights in the recognition profile and Z-scores of candidate sites were calculated as the sum of the respective positional nucleotide weights . The threshold for the site search was defined as the lowest score observed in the training set (Z-score = 4.8). The sequence logo for the consensus Zur-binding motif in Actinobacteria was constructed using WebLogo 2.0 . The phylogenetic trees were constructed by the maximum likelihood method implemented in the PROML program of the PHYLIP package  using multiple sequence alignments of protein sequences produced by the Clustal W2 program . The deduced regulatory interactions were stored in the CoryneRegNet database .
The authors thank Eva Trost for providing data from the C. aurimucosum genome project prior to publication and Peter Heimann for help with fluorescence microscopy. The work of DAR was supported by a grant from the Russian Academy of Sciences (program "Molecular and Cellular Biology").
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