Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria
© Valencia et al.; licensee BioMed Central Ltd. 2013
Received: 16 October 2012
Accepted: 21 March 2013
Published: 11 April 2013
Heavy metal Resistance-Nodulation-Division (HME-RND) efflux systems help Gram-negative bacteria to keep the intracellular homeostasis under high metal concentrations. These proteins constitute the cytoplasmic membrane channel of the tripartite RND transport systems. Caulobacter crescentus NA1000 possess two HME-RND proteins, and the aim of this work was to determine their involvement in the response to cadmium, zinc, cobalt and nickel, and to analyze the phylogenetic distribution and characteristic signatures of orthologs of these two proteins.
Expression assays of the czrCBA operon showed significant induction in the presence of cadmium and zinc, and moderate induction by cobalt and nickel. The nczCBA operon is highly induced in the presence of nickel and cobalt, moderately induced by zinc and not induced by cadmium. Analysis of the resistance phenotype of mutant strains showed that the ΔczrA strain is highly sensitive to cadmium, zinc and cobalt, but resistant to nickel. The ΔnczA strain and the double mutant strain showed reduced growth in the presence of all metals tested. Phylogenetic analysis of the C. crescentus HME-RND proteins showed that CzrA-like proteins, in contrast to those similar to NczA, are almost exclusively found in the Alphaproteobacteria group, and the characteristic protein signatures of each group were highlighted.
The czrCBA efflux system is involved mainly in response to cadmium and zinc with a secondary role in response to cobalt. The nczCBA efflux system is involved mainly in response to nickel and cobalt, with a secondary role in response to cadmium and zinc. CzrA belongs to the HME2 subfamily, which is almost exclusively found in the Alphaproteobacteria group, as shown by phylogenetic analysis. NczA belongs to the HME1 subfamily which is more widespread among diverse Proteobacteria groups. Each of these subfamilies present distinctive amino acid signatures.
From a physiological point of view, metals fall into three main categories, namely essential and non-toxic (e.g. Ca2+ and Mg2+); essential, but harmful at high concentrations (e.g. Fe2+, Mn2+, Zn2+, Cu2+, Co2+, Ni2+ and Mo2+), and toxic (e.g. Hg2+ or Cd2+) . However, at high concentrations, both essential and nonessential metals can be harmful to the cell, damaging the cell membrane, the structure of DNA, or changing the specificity of enzymes [2–4]. The microorganisms have developed homeostasis systems in order to maintain an optimal intracellular concentration of metals. This is achieved through controlling the processes of transport, intracellular trafficking, efflux and conservation, ensuring its bioavailability to cellular processes and preventing damage to cellular components .
Studies support a role for horizontal gene transfer (HGT) in the evolution of metal homeostasis in Proteobacteria, along with the identification of putative genomic islands (GIs), with examples in Cupriavidus metallidurans, Pseudomonas putida KT2440 and Comamonas testosteroni S44 [6–9]. In fact, many microorganisms have genes located on chromosomes, plasmids, or transposons encoding specific traits conferring resistance to a variety of metal ions .
Efflux is one of the main approaches used by bacteria to control internal metal ion concentrations, and several efflux systems have been described in bacteria. The P-type ATPases use ATP hydrolysis to promote ion transport and have been identified in efflux of both mono- and divalent cations from the cytoplasm [10–13]. The Cation Diffusion Facilitator (CDF) are chemiosmotic ion/proton exchangers that present six transmembrane helices and are involved in the efflux of divalent metal cations [11, 14, 15].
In Gram-negative bacteria, the Resistance-Nodulation-Division superfamily (RND) includes systems that confer resistance to antibiotics and metals, and it is composed of a tripartite protein complex: an RND protein, located in the cytoplasmic membrane, a periplasmic membrane fusion protein (MFP) and an outer-membrane channel protein (OMP) [16–18]. These components form a channel that spans both membranes and the periplasmic space [18–21]. Based on the nature of their substrate, the RND superfamily was divided into seven families, of which the hydrophobe/amphiphile efflux (HAE), and the heavy-metal efflux (HME) have been extensively studied [17, 22]. Nies further subdivided the HME-RND proteins into sub-groups, according to the substrate they transport: HME1 (Zn2+, Co2+, Cd2+), HME2 (Co2+, Ni2+), HME3a (divalent cations), HME3b (monovalent cations), HME4 (Cu+ ou Ag+) and HME5 (Ni2+) .
The cytoplasmic membrane RND proteins have 12 transmembrane alpha helices (TMH), among which TMH IV contains amino acid residues that are conserved in most RND proteins . The HME1-RND and HME2-RND have the same motifs, DFG-DGA-VEN, present in proteins CzcA (HME1) or CnrA and NccA (HME2) [14, 23]. Both aspartate residues and the glutamate residue in TMH IV of CzcA are required for proton/substrate-antiport, suggesting that they are probably involved in proton translocation [14, 23, 24]. A model for cation transport by an HME-RND was recently proposed for the copper transporter CusA, in which the metal ion moves along a pathway of methionine residues, causing significant conformational changes in both the periplasmic and transmembrane domains . These systems are proposed to promote the efflux of both cytoplasmic and periplasmic substrates, transporting of the substrate either via the RND protein or in some cases via the membrane fusion protein with the aid of periplasmic metal chaperones [14, 24].
The best characterized RND heavy metal efflux systems are mainly those from Cupriavidus (previously called Ralstonia and Alcaligenes): CzcCBA (Cd2+, Zn2+, and Co2+ resistance) from Ralstonia metallidurans CH34 [26–28]; CnrCBA (Ni2+ and Co2+) from Ralstonia eutropha[29, 30]; NccCBA (Ni2+, Co2+ and Cd2+) from Alcaligenes xylosoxidans 31A . However, other systems such as Pseudomonas aeruginosa Czr (Cd2+ and Zn2+ resistance) ; and Helicobacter pylori Czn (Cd2+, Zn2+ and Ni2+ resistance) were also studied .
In order to better understand the role of the RND efflux systems in the export of divalent cations in other Proteobacteria, we investigated the role of two HME-RND systems present in the Alphaproteobacterium Caulobacter crescentus. A previous bioinformatics analysis made by Nies (2003) through comparison of the genomes of 63 prokaryotes (Archaea and Bacteria) with the genome of C. metallidurans, identified seven ORFs encoding putative RND proteins in C. crescentus CB15 of which two, CC2724 (corresponding to CCNA_02809 in the derivative strain NA1000; here called CzrA) and CC2390 (CCNA_02473; here called NczA), belong to the HME subgroup. Previous works from our group  identified that the czrCBA locus is involved in resistance to cadmium and zinc and is induced by these cations, and other reports  confirmed that this operon is induced by cadmium.
In this work, we have characterized both of these systems by constructing null mutant strains of the respective RND-encoding genes and evaluating their resistance to cadmium, zinc, cobalt and nickel. We have also studied the pattern of gene expression of both operons in response to each metal. The results showed that the two proteins have different responses to metals both in resistance and in expression, suggesting distinct but somewhat overlapping roles for each protein. Moreover, a phylogenetic analysis showed that these proteins belong to two distinct clusters, and that each group presents distinctive amino acid signatures.
Results and discussion
Comparative analysis of czr and nczclusters
Amino acid alignments showed that these paralogous share very low overall identity: CCNA_02806 and CCNA_02471 (CzrC and NczC, outer membrane factor), 36% identity; CCNA_02807 and CCNA_02472 (CzrB and NczB, membrane fusion protein), 28% identity; and CCNA_02809 and CCNA_02473 (CzrA and NczA, RND protein) 56% identity. Moreover, the czr locus contains three additional genes encoding putative hypothetical proteins (CCNA_02805, CCNA_02808 and CCNA_02810). Orhtologues of CCNA_02805 are found in this locus in Phenylobacterium zucineum and in Stenotrophomonas maltophilia, but no orthologs of CCNA_02808 are found in this locus outside of the Caulobacteraceae. The CCNA_02810 is a putative ATP-binding conserved protein that possesses a domain of unknown function. The low similarity among proteins encoded in these two loci suggests that they have diverged substantially, and that they may have acquired specialized roles in maintaining metal homeostasis.
Identification of czr and nczpromoter regions
To confirm that CCNA_02805 belongs to the czrCBA operon, an RT-PCR analysis was carried out using primers within the predicted coding regions of CCNA_02805 and czrC (Figure 2B). The results confirmed that there is a transcript encompassing CCNA_02805 and czrC. Since there are no gaps between czrC-czrB and czrB-czrA (the same goes for nczCBA), we conclude that at least these genes belong to putative operons. We cannot exclude the possibility that CCNA_02811 (encoding a putative Cd2+/Zn2+-exporting P-type ATPase) is co-transcribed with czrCBA, although the distance between CCNA_02810 and CCNA_02811 is 63 bp. These results agree with the results reported previously that transposon insertions into either CCNA_02805, CCNA_02807 or CCNA_02809 caused a similar phenotype of increased sensitivity to cadmium .
Determination of gene expression in response to metals
These results suggest that these two RND efflux systems have different roles in response to metal. The czr operon seems to be important mainly for the response to cadmium and zinc, whereas the ncz operon for the response to cobalt and nickel, since it was highly and quickly induced by these metals. A whole-genome transcriptional analysis upon heavy metal stresses (chromium, cadmium, selenium, and uranium) showed that the cluster CCNA_02806-CCNA_02812 (including the czr operon and a gene encoding a P-type ATPase) is highly induced in response to cadmium . In our previous work, β-galactosidase assays using the lacZ gene from the inserted transposon showed an induction of all genes by cadmium after 24 h . The present work confirmed previous data for the czr regulation by zinc and cadmium, and further demonstrated that it is also induced by nickel and cobalt to a minor degree. This is also the first determination of the ncz operon induction by cobalt and nickel.
Roles of each HME-RND system in metal resistance
These data, taken together with the expression profile of each operon, indicate that czrA is responsible mainly for cadmium and zinc efflux and has a secondary role in resistance to cobalt, whereas nczA is responsible mainly for nickel, and cobalt efflux with a secondary role in resistance to zinc and cadmium. To confirm the involvement of czrA and nczA in metal resistance, complementation analyses were performed for each gene. The strains harbouring the empty vector or the vector with the complementing copy of each gene were grown in PYE-kanamycin medium supplemented with 0.2% xylose and addition of the metal tested for gene induction. Figure 4B shows that complemented strains were able to grow similarly to NA1000 strain, whereas ΔczrA strain did not grow in CdCl2 and ZnCl2, and the ΔnczA strain presented reduced growth in the presence of ZnCl2, CoCl2 and NiCl2.
The presence of two related transport systems in the genome suggests that they would improve the capacity of C. crescentus to resist to high concentration of metals, agreeing with the notion that they are complementary in function.
Characterization and distribution among proteobacteria
The CCNA_02805-02810 cluster is located at the end of a 60-kb genomic island, identified in the annotation of the corresponding strain C. crescentus CB15 genome , indicating that at least one of these C. crescentus RND efflux system may have been acquired by horizontal gene transfer. This confirms a common association of these genes to mobile genetic elements, as discussed for other bacteria [7, 8].
We observed no correlation between the two phylogenetic groups A and B and the response to different types of metals of the RND proteins already characterized. C. crescentus NczA, which is important for nickel and cobalt resistance, clustered in group A with C. metallidurans CH34 CzcA, which is involved in Cd2+/Zn2+/Co2+ resistance [26–28]. Similarly, C. crescentus CzrA, important for Cd2+/Zn2+ resistance, clustered in group B with CnrA from C. metallidurans CH34, which confers resistance to Ni2+ and Co2+, and with NccA from A. xylosoxidans 31A which confers Ni2+/Co2+/Cd2+ resistance [31, 41]. It must be noticed, however, that we observed two separate branches within group A (Figure 5), which include different genera of the gamma-Proteobacteria and only one contains protein sequences from beta-Proteobacteria (such as C. metallidurans CzcA). We cannot exclude the possibility that these two sub-groups could show some correlation with metal specificity, but more experimental work with representative proteins from each group is necessary to clarify that.
In order to localize the identified signatures in the CzrA protein structure, we performed a homology modeling analysis utilizing the structure of E. coli CusA as model (PDB: 3 k07), since it is the only metal-transporting RND protein structure so far available in the data bases. All of the motifs described above, with the exception of MV, are located in the periplasmic domain of CzrA structural model (Figure 6C). MV is located in TM8 in CzrA (Figure 6C), which in E. coli CusA suffers a significant conformational change when it binds Cu+ or Ag+, and was proposed to be involved in transmembrane signaling and in initiation of proton translocation across the membrane . MI and MII are located in two close loops in the sub-domain PN1, MIII is located in the sub-domain DN and MIV is located in the sub-domain-PC2 (Figure 6C). The PC2 sub-domain in E. coli CusA was proposed to move, creating a cleft between PC1 and PC2 when CusA binds to Cu+ or Ag+.
The most conspicuous difference between the CzrA and NczA groups is the length of the loop located in PN2, called here Large Loop for CzrA and Small loop for NczA. The periplasmic PN2 region is involved in the interaction between E. coli CusA and one molecule of the CusB dimer [25, 45]. When we superimpose the CzrA model on the CusAB2 complex structure (PDBID: 3NE5), the results suggest that the Large Loop could affect the interaction between CzrA and the adaptor protein (not shown). The predicted adaptors for the C. crescentus HME-RND systems, CzrB and NczB, share no significant amino acid sequence identity with CusB . Nevertheless, most of the interface residues at the sub-domain DC in CusA involved in the interaction with one molecule of the CusB dimer are conserved in the CzrA and NczA orthologs, although the two residues located in PN2, D155 and R147, are not conserved in members of either group. We have to take into consideration the fact that the structures of the two partners have not been experimentally determined, and therefore one cannot infer how the interaction between the adaptors and the RND proteins takes place.
Correlation between some relevant residues in E. coli CusA with the corresponding residues in the CzrA and NczA orthologs
Residue conserved b
Q ( Q )
D ( D )
L ( L )
In this work, we show a comparison of two HME-RND family efflux systems (czrCBA and nczCBA), where the RND proteins (CzrA and NczA) have the motif DFG-GAD-VEN involved in the export of metal divalent cations. Gene expression analyses, as well as metal resistance profile of mutant strains, showed that czrA is involved mainly in response to cadmium and zinc with a secondary role in response to cobalt, whereas the nczA is involved mainly in response to nickel and cobalt, with a secondary role in response to cadmium and zinc. Phylogenetic analysis of these two RND proteins showed that they group into separate branches, and that CzrA-like proteins (HME2 group) are mainly found in the Alphaproteobacteria, while NczA-like proteins (HME1 group) are more widespread among Proteobacteria. Signature motifs of each group were identified, but no correlation between phylogenetic distribution and the response to different types of metals was observed.
Bacterial strains, plasmids and growth conditions
Bacteria strains and plasmids used in this study
Strains or plasmids
Source or reference
Transformation recipient strain
Conjugation donor strain
Also CB15N, synchronizable derivative of wild-type CB15
NA1000 ΔnczA (ΔCCNA_02473)
NA1000 ΔczrA (ΔCCNA_02809)
Cloning vector; Ampr
pRK2-derived vector with a promoterless lacZ gene; Tetr
Suicide vector used for gene disruption containing oriT and sacB; Kanr
xylX locus in pNPT228; Kanr
Cloning of the promoter regions and β-galactosidase activity assays
Primers used in this study
Sequence (5′- → 3′)a
Growth phase-dependent promoter activity was measured by β-galactosidase assays , from exponential or stationary phase (24 h) cultures grown in PYE-tetracycline. Expression driven from promoters Pczc1 and Pczc2 was also evaluated in the presence of divalent cations (Sigma) at the following concentrations: 10 μM CdCl2; 100 μM ZnCl2; 100 μM CoCl2; or 100 μM NiCl2. Cultures grown in PYE-tetracycline at 30°C were diluted to an initial optical density at 600 nm (OD600) of 0.1, and the divalent metal was added when they reached OD600 0.5. Aliquots were taken before and at several time points after metal addition and expression was measured by β-galactosidase assays. Statistical treatment of the data was carried out using Student’s T-Test.
Total RNA from exponentially growing C. crescentus NA1000 cells was extracted by the Trizol method, as described by the manufacturer (Life Technologies). RNA obtained was treated with 0.6 U of RQ1 DNase (Promega) for 30 min at 37°C, followed by phenol extraction and ethanol precipitation, in order to eliminate contaminating genomic DNA. The RNA integrity was assessed by agarose/formaldehyde gel electrophoresis and quantified in a Nanodrop 2000 device (Thermo Scientific). The reactions were performed using primers RND3 and RND4 (located within the coding region of CCNA_02805 and CCNA_02806, respectively). cDNA was synthesized from 0.25 μg of RNA using Super Script™ First Strand Synthesis System (Life Technologies) in a 20 μl final volume, following the manufacturer’s instructions. PCR amplification was performed using 1.2 μg of cDNA as template, 10 pmol each primer, 5% DMSO in a final volume of 25 μl using Taq DNA polymerase (Fermentas). The PCR conditions were: 94°C for 5 min, followed by 30 cycles of 94°C for 30 s, 45°C for 30 s, and 72°C for 1 min, with a final cycle at 72°C for 5 minutes. A negative control reaction was performed as described above, without the addition of reverse transcriptase. The PCR products were analyzed on 1% agarose gel electrophoresis.
Construction of the czrA and nczAmutant and complemented strains
In-frame deletions were constructed by allelic exchange using the pNPTS138 suicide vector and C. crescentus NA1000 strain. Two genomic regions upstream and downstream of the gene to be deleted were amplified by PCR using pfx Platinum DNA polymerase (Life Technologies) and primers RND7/RND8 (785 bp, HindIII/EcoRI) and RND9/RND10 (752 bp, EcoRI/MluI) to czrA gene and primers RND11/RND12 (870 bp, HindIII/BamHI) and RND13/RND14 (654 bp, BamHI/MluI) to nczA gene. A terminal adenine was added with Taq DNA Polymerase (Life Technologies) and subsequently the fragments were cloned into vector pGEM-T Easy (Promega). The fragments were cloned in tandem into the pNPTS138 vector, the plasmids were transferred to C. crescentus strain NA1000 by conjugation with E. coli S17-1, and recombinant colonies were selected in PYE-kanamycin plates. A colony containing the integrated plasmid was inoculated in PYE medium without antibiotics for 48 hours, and loss of the plasmid was selected in PYE media containing 3% sucrose. The deletions were confirmed by PCR. Double mutant ΔczrAΔnczA was obtained by introducing the pNPTS138 vector containing the 5′ and 3′-flanking regions of czrA into the ΔnczA strain. PCR products using primers RND15/RND16 (3243 bp) and RND17/RND18 (3132 bp), containing the coding regions of czc1 and czc2 genes respectively, were used to generate complemented strains. Each fragment was cloned into the suicide vector pNPT228XNE, and the plasmid was inserted into the mutant strains by conjugation with E. coli S17-1. The insertion of the recombinant vector occurs at the xylose utilization locus, and expression of the cloned genes is induced with 0.2% xylose.
Growth assays in the presence of metals
Initial cultures at OD600 = 0.05 in PYE medium were divided into tubes containing or not each metal (40 μM CdCl2, 100 μM ZnCl2, 100 μM CoCl2 and 300 μM NiCl2), and incubated at 30°C for 24 h with agitation. Growth was determined by measuring the OD600 of the cultures.
C. crescentus NA1000 and mutant strains carrying either the empty vector pNPT228XNE or the vector harbouring either czrA or nczA genes were grown in PYE-kanamycin at 30°C with agitation to an OD600 of 0.3. Samples of 10 μl were streaked on PYE-kanamycin plates containing 2% xylose and with or without addition of each of the following metal salts: 35 μM CdCl2, 130 μM ZnCl2, 50 μM CoCl2 and 280 μM NiCl2, and plates were incubated at 30°C for 3 days. Statistical treatment of the data was carried out using Student’s T-Test.
Phylogenetic and protein structure analyses
Amino acid sequences presenting more than 55% identity with CzrA and NczA were used as an imput for CLUSTALX . The complete list of the protein sequences used is found in Additional file 1: Table S1. The phylogenetic tree was constructed by a neighbor-joining method with 1000 bootstrap replicates using the CLUSTALX program. The multiple sequence alignment was used to create the logo representation of the CzrA and NczA orthologous grups. The figure was generated using the WebLogo server  and the height of the residue symbol indicates the degree of conservation. The sequence numbering shown below the logo corresponds to the proteins from C. crescentus NA1000.
Homology modeling of CzrA was performed using the PHYRE2  using as a three-dimensional structural template the chain A of E. coli CusA [PDB: 3 k07; . CzrA and CusA share 33% sequence identity. The model generated has 100% confidence and 93% coverage. The result was analyzed with the PyMOL Molecular Graphics System, Version 1.5 Schrödinger, LLC .
This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP). EYV was supported by doctoral fellowship from CNPq. VSB was supported by postdoctoral fellowship from FAPESP. MVM was partially supported by CNPq.
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