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Journal of Bacteriology, January 2008, p. 21-27, Vol. 190, No. 1
0021-9193/08/$08.00+0 doi:10.1128/JB.01389-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Unité des Membranes Bactériennes Institut Pasteur (CNRS URA 2172), 25 Rue du Dr. Roux, Paris Cedex 15, France
Received 27 August 2007/ Accepted 10 October 2007
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In gram-positive bacteria, cell-wall-anchored surface proteins bind heme and/or hemoproteins and transfer heme to ABC transporters that internalize it through the plasma membrane using ATP hydrolysis as an energy source (19).
In gram-negative bacteria, heme sequentially crosses the two membranes. Both steps are energy-dependent processes. Transport through the outer membrane involves specific surface-exposed receptors powered by the proton motive force supplied by an inner membrane machine: the TonB-ExbB-ExD multiprotein complex (11). Transport through the inner membrane involves periplasmic binding protein-dependent ABC transporters energized by ATP hydrolysis (17, 31).
Whereas gram-positive heme surface receptors are heterogeneous, gram-negative heme outer membrane receptors belong to a family of TonB-dependent transport (TBDT) receptors that comprises heme, hemoproteins, hemophore, ferrisiderophore, B12 vitamin, transferrin, and lactoferrin receptors. X-ray crystal structures have been determined only for a few siderophore receptors, but three-dimensional modeling has predicted that other receptors belonging to this family may have a similar folded structure. Known three-dimensional structures show a plug inside a β-barrel organization. The N-terminal plug domain closes the receptor pore and is exposed to the periplasm, where it can make contact with TonB (10). Binding of the ferrisiderophores triggers conformational changes in the plug domain, leading to formation of a channel for the ligand.
In addition, many outer membrane receptors involved in iron uptake (for citrate, pyoverdin, heme, and hemophore) are positively regulated by their ligand via extracytoplasmic function sigma factors and membrane-bound anti-sigma factors (5). These receptors have an extra N-terminal domain ranging from 50 to 100 amino acids, referred to as the signaling domain. The signaling cascade also requires the TonB complex. Ligand binding to its cognate receptor induces a TonB-dependent conformational change in the signaling domain that releases extracytoplasmic function sigma from anti-sigma inhibition and thereby leads to transcription of the receptor gene-containing operon (5).
Whereas receptors have a low degree of primary sequence homology, reflecting the diversity of ligands, the TonB/ExbB-ExbD complex is highly conserved and is able to energize several receptors. The TonB protein interacts directly with the receptors, whereas ExbB and ExbD make contact between themselves and with the TonB membrane anchor, playing a role in TonB stabilization and energy conveying to the outer membrane (27). The interactions between TonB and the TBDT receptors involve the carboxy terminus of TonB and several regions of the receptors. Genetic and structural studies have revealed the crucial role of contact between the third and fourth TonB β strands and a short peptide at the N terminus of the receptors named the TonB box, which is conserved on all receptors. Such an interaction has been visualized in two Escherichia coli TonB-receptor cocrystal structures as a β-strand exchange between the two protein segments (26, 30). Other interactions between TonB and the TBDT receptors involve several periplasmic loops on the receptors (26).
Genes encoding TonB, ExbB, and ExbD are present in all thus-far-sequenced gram-negative genomes. They display diverse types of genetic organization. Genes exbB and exbD are usually linked and located in one iron-regulated operon. Occasionally, tonB is clustered with exbB-exbD or with genes encoding ferrisiderophore or heme uptake systems. Unlike E. coli, which has a unique set of tonB-exbB-exbD genes, some bacteria have several paralogs, not all of them functional. Vibrio cholerae has one TonB-ExbB-ExbD system encoded by the larger replicon which is able to complement an E. coli tonB mutation for most TBDT receptor-mediated functions (23). A second TonB-ExbB-ExbD machine is encoded by the smaller V. cholerae replicon, which is located in the heme permease hutBCD operon (23). Both systems exhibit redundant functions for heme and siderophore uptake, with some distinct specificities. The TonB1 system is required for schizokinen uptake, and TonB2 is required for enterobactin utilization (29). The TonB1 system allows the use of heme at a wide range of medium osmolarities, whereas TonB2 promotes heme uptake only at low osmolarity (21). In Vibrio anguillarum, two TonB systems function in iron uptake, but only one is essential for virulence (32). In V. cholerae and V. anguillarum, the TonB2 complex requires an additional protein named TtpC (32). In Pseudomonas aeruginosa, several TonB-ExbB-ExbD complexes have been characterized. However, most heme and iron uptake functions rely on a TonB1 set (33). A third TonB was shown to be required for normal twitching mobility and extracellular assembly of type IV pili (14). In Actinobacillus pleuropneumoniae, two TonB systems are also present, and one was shown to be more important for virulence (1).
Serratia marcescens DNA sequence analysis has indicated the presence of several tonB-exbB-exbD genes (six tonB paralogs and two exbB-exbD pairs). Among their products, two TonB proteins have been shown to be functional: S. marcescens TonB (TonBSm) and HasB. TonBSm is encoded by a gene unlinked to any exbB-exbD genes or to any iron/heme transport genes. When expressed in E. coli, it complements most E. coli TonB (TonBEc) natural functions (12). HasB is encoded by a gene located in the has operon dedicated to hemophore-bound heme acquisition (25). This operon encodes HasR, the hemophore outer membrane receptor which is also a heme receptor; HasA, the hemophore; and HasD and HasE, inner membrane components of the type I secretion system required for HasA secretion and HasB. The has operon is negatively regulated by iron and positively regulated by a sigma anti-sigma (HasI-HasS) signaling cascade triggered by heme-loaded hemophore binding to HasR. The Has system is functional in an E. coli recombinant strain for free or hemophore-bound heme uptake and for hemophore-mediated positive regulation (2, 13). Both heme transport and heme signaling are dependent on the host TonB-ExbB-ExbD complex (13, 28). TonBSm complements the TonBEc protein for heme transport and heme signaling. In a previous work, we showed that HasB6, a HasB allele mutated in its transmembrane domain so as to be functional in E. coli, complements the TonBEc protein for heme transport and heme signaling via the Has system (25). However, HasB6 does not complement other TonB functions such as iron siderophore uptake,
80 infection, or killing by colicin B. These results showed that HasB6 was specific to heme uptake and raised the question of the target of this specificity. HasB6 could be specific to heme TBDT receptors. At least one heme receptor other than HasR is present and functional in S. marcescens, since hasR mutants are still able to use heme, albeit less efficiently than a wild-type strain. Alternatively, HasR-HasB could form a specific pair. In S. marcescens, the iron regulation of HasR and HemR receptors and the presence of several TonB paralogs complicate the study of each TonB function. Thus, experiments were performed in E. coli.
In the present study, we have cloned, in E. coli, another heme receptor, HemR. We show that this receptor is functional and TonB dependent and does not function with HasB6, thereby demonstrating that HasB is not dedicated to heme TBDT receptors but rather forms a specific pair with HasR.
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TABLE 1. Strains and plasmids used in this study
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-aminolevulinic acid (ALA) were obtained from Sigma Chemical. The hemoglobin concentration was calculated on the basis of the heme monomer. Hemin and hemoglobin solutions were filter sterilized with 0.45-µm-pore-size Millipore filters. Strains were grown on LB medium (22) aerobically at 30 or 37°C. When required, ALA was used at a concentration of 20 µg ml–1. Iron-depleted medium was obtained with the addition of Dip at a 0.2 mM final concentration. Antibiotics were added to the following final concentrations (µg ml–1): ampicillin, 100; spectinomycin, 100; chloramphenicol, 20; kanamycin, 25; streptomycin, 100; and tetracycline, 10. Solid media contained 1.5% Difco agar. Soft LB agar medium contained 0.7% Difco agar. Growth assays on agar plates supplemented with purified HasA. A 100-µl sample of an overnight culture of the tested strain was mixed with 4 ml of soft agar and poured onto LB plates supplemented with 10–7 hemoglobin. Wells (5 mm in diameter) were cut in the agar and filled with 100 µl of sterile HasA (10–5, 10–6, or 10–7 M) prepared from a C600(pSYC34) culture supernatant as described previously (28). Growth around the wells was recorded after overnight incubation at 37°C.
Genetic techniques. P1 lysates and transductions were performed as described by Miller (22). Cells were transformed by the calcium chloride method (18) or electroporation (8).
DNA manipulations. Chromosomal DNA was isolated by using the Wizard genomic DNA purification kit (Promega catalog no. A1120). Large-scale plasmid DNA preparations were made by using a Plasmid Maxi kit (Qiagen, Inc., Germany) as recommended by the manufacturer. Small-scale plasmid DNA preparations were done by using a QIAprep Spin Miniprep kit (Qiagen). Restriction, modification, and ligation were carried out according to the manufacturer's recommendations. DNA fragments of interest were separated by gel electrophoresis and isolated using a QIAquick gel extraction kit (Qiagen). DNA fragments were amplified in a Hybaid PCR thermocycler, using LA Taq (TaKaRa, Japan).
Nonpolar deletion of hemR in S. marcescens by red linear DNA gene inactivation.
A nonpolar mutation that deletes the entire hemR gene was created by allelic exchange using a method already described (7). Briefly, plasmid pKOBEGA (an ampicillin-resistant derivative of pKOBEG [see Table 1]) was introduced into the target strain, and electrocompetent cells were prepared at 30°C after induction of the
red system carried by pKOBEGA with 0.2% arabinose. A three-step PCR procedure was used to produce a PCR product in which the cat gene from pHP45
(9) is flanked by 500-bp homology arms corresponding to DNA regions located upstream and downstream from the hemR start and stop codons, respectively. The following primers were used: for the left 500-bp hemR homology arm, hemR.500-5 (5'-ACCGCATCGAAAGCTTGCTGAAATAAC-3') and hemR.cat.L-3 (5'-GCGGATGAATGGCAGAAATTGGTGCAACTCTCCGTATGTA-3'), and for the right 500-bp hemR homology arm, hemR.500-3 (5'-ACCTCTTACGTGCCGATCAATTGACTATCTGGCGGACAACCCGG-3') and hemR.cat.L-5 (5'-ACCAGCGCCATCCAGGCCGGC-3').
The cat gene cassette (0.9 kb) was amplified from strain E. coli FB8 (ttdA::Cm) (24) using the primers cat-5 (5'-AATTTCTGCCATTCATCCGC-3') and cat-3 (5'-TTGATCGGCCGTAAGAGGT-3'). The PCR product resulting from the three-step procedure was introduced into S. marcescens SMH3/pKOBEGA using electroporation, and chloramphenicol-resistant deletion mutants produced by allelic exchange were selected at 37°C (to eliminate the thermosensitive plasmid pKOBEGA). Correct chromosomal insertion was checked by PCR amplification using the cat primers cat-3 and cat-5 in combination with hemR.500-3 and hemR.500-5, respectively.
Cloning of hemR. The S. marcescens strain DB11 hemR DNA sequence was obtained from the S. marcescens genomic sequence database (http://www.sanger.ac.uk/Projects/S_marcescens/). A 2,202-bp DNA fragment corresponding to the hemR gene on the S. marcescens DB11 chromosome was amplified using forward and reverse primers hemR-5 (5'-GGCAGCCAGCAAAGCTTTTGATATGTTT-3') and hemR-3 (5'-ATTTTGGCCTGTTGGTACCGTTCGTATAG-3'). PCR products were digested with HindIII and KpnI and ligated to pAM239 digested with HindIII and KpnI to create pAM339-hemR. The sequence of hemR inserted in plasmid pAM239-hemR was compared to the S. marcescens genomic sequence database.
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HemR is functional for heme uptake in S. marcescens. As already described, disruption of the hemophore-dependent heme receptor hasR in S. marcescens decreased but did not abolish the capacity for heme uptake (28). We hypothesized that hemR was responsible for has-independent uptake of heme. We disrupted hemR in an S. marcescens heme auxotroph SMH3 hasR mutant using a nonpolar gene substitution method as described in Materials and Methods. The SMH3 (hasR hemR) mutant obtained was tested for growth in the presence of exogenous hemoglobin at a final concentration of 10–5 M. As shown in Table 2, the SMH3 strain and its hasR derivative were able to take up heme and to grow. In contrast, S. marcescens SMH3 (hasR hemR) was unable to take up heme or to grow. This demonstrates that hemR coded for the alternative heme outer membrane receptor of S. marcescens. The hemR structural gene from S. marcescens was amplified, cloned in low-copy-number plasmid pAM239, and introduced into strain SMH3 (hasR hemR). The resulting strain, SMH3 (hasR hemR)/pAM239-hemR, was able to take up heme and to grow in the presence of hemoglobin (10–5 M) (Table 2). The latter validated the identification of HemR as a heme outer membrane receptor.
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TABLE 2. Heme uptake in S. marcescens strain SMH3 and its derivatives impaired in heme uptake systemsa
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hemA) and tested growth stimulation of the transformant strains with heme or hemoglobin. Deletion of hemA, which abolishes ALA biosynthesis, enabled E. coli growth only in the presence of ALA. Addition of exogenous heme did not restore the growth of strain C600 (
hemA), since E. coli was unable to use exogenously supplied heme in the absence of a heterologous outer membrane heme transporter. As shown in Table 3, growth stimulation by exogenous hemoglobin was observed with strain C600 (
hemA) harboring a plasmid expressing hemR. Similar results were obtained with free heme (data not shown). These results show that HemR alone allowed heme transport across the outer membrane in E. coli and its use as a porphyrin source. |
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TABLE 3. Heme uptake in E. coli strain C600 ( hemA) expressing hemR from S. marcescensa
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hemA)/pAM239-hemR abolished growth in the presence of hemoglobin (Table 4). This indicated that heme transport through HemR was dependent on the TonB-ExbB-ExbD complex, since it is also the case for HasR. As shown in Table 4, introduction of a plasmid expressing either TonBEc or TonBSm in strain C600 (
hemA tonB)/pAM239-hemR or strain C600 (
hemA tonB)/pAM238-hasR restored heme uptake. In contrast, a plasmid expressing HasB6 enabled the heme utilization of C600 (
hemA tonB)/pAM238-hasR but not of C600 (
hemA tonB)/pAM239-hemR. These results showed that HasB6 was specific to the HasR-dependent heme uptake system and not to heme receptors in general. |
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TABLE 4. Complementation of a tonB mutation for HemR- and HasR-dependent heme uptake in E. coli strain C600 ( hemA tonB) harboring pUC19 derivatives expressing tonBEc, tonBSm, or hasB6a
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45-125) was used. For these experiments, we used fur isogenic strains to avoid the deleterious effect of dipyridyl addition on tonB mutant growth. The mutant HasR
45-125 has a wild-type phenotype for heme uptake but is unable to initiate the has signaling cascade in the presence of a heme-loaded hemophore (2). The results presented in Table 5 show that this mutant receptor enabled hemophore-dependent and hemophore-independent heme acquisition as efficiently as did the wild-type receptor in the presence of HasB6. This clearly demonstrated that the specificity of HasB6 toward HasR was not related to the presence of a signaling domain. Surprisingly, with TonBEc, HasR
45-125 slightly stimulated hemophore-dependent heme uptake, whereas entire HasR had no effect (Table 5). |
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TABLE 5. Complementation of the tonB mutation for free and hemophore-dependent heme uptake in E. coli strain C600 ( hemA) expressing HasR and HasR 45-125a
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We identified a heme receptor paralog in the S. marcescens genomic sequence (hemR). We inactivated hemR with a nonpolar insertion in S. marcescens. Using single and double hemR-hasR mutants, we showed that, whereas each hasR or hemR single mutant is still able to acquire heme, the hemR hasR double mutant has completely lost this uptake capacity, demonstrating that hemR is functional in S. marcescens. When cloned into E. coli, hemR enables heme transport through the outer membrane in a TonB-dependent manner. HasB6 is unable to replace TonB for heme uptake via HemR. HasB is not dedicated to heme receptors in general but is specific to HasR. In fact, heme receptors do not form a homogeneous family. Amino acid comparison between them shows that heme receptors share homologies ranging from 20 to 90% identity. The HasR subfamily is only distantly related to other heme receptors. S. marcescens HemR and HasR share 23% identity and 37% similarity, values that are not significantly higher than the homologies shared with TBDT receptors involved in other types of iron source uptake. However, HasR and HemR strongly differ in their N termini, since HasR, which belongs to the family of autoregulated receptors, possesses an N-terminal extension, the signaling domain. We show here that HasR lacking the entire signaling domain is equally functional with TonB and HasB6. This demonstrates that the N-terminal extension is not required for the activation of HasR by HasB. Nevertheless, we observed that truncated HasR lacking its signaling domain, when energized by TonB, is more efficient at heme-hemophore uptake than the entire HasR protein. This discrepancy is not visible for heme uptake, which requires lower TonB expression (16). On the other hand, the
45-125 deletion does not enhance HasB6 activity. These results suggest that the N terminus extension restricts the access of the energizing protein. The absence of an effect of the HasR signaling domain upon HasB6 activity can be explained either by other contacts between the two proteins or by a higher affinity of HasB6 for HasR, resulting in full HasB6 activity even with fewer HasR binding sites available.
Interactions between TonB proteins and TBDT receptors involve their TonB C-terminal domain. This domain, poorly conserved between HasB and the other TonB proteins, was shown to contact the TonB boxes in BtuB-TonB and FhuA-TonB structures. The putative TonB boxes of HemR (DETMTVVA) and HasR (DSLTVLGA) are equally similar to the E. coli TBDT receptor TonB box consensus (DTLVVTA). It is thus unlikely that HasB specificity relies on the interaction between HasB and the HasR TonB box. Moreover, TonB boxes have been shown to be essential for ligand transport and ligand-mediated signaling but not for specificity. TonB box switching between an E. coli receptor (ChuA) and the V. cholerae receptor HutA, each of which functions only with the TonB protein from their original host, does not switch TonB dependency (20). Sequence comparison reveals that HasB is ca. 27% identical to TonBSm and 29% identical to TonBEc. HasB (263 amino acids) is longer than TonBSm (247 amino acids) and TonBEc (239 amino acids), indicating that HasB has a longer central proline-rich spacer. Also, the third "TonB β-strand," located between amino acids 252 and 258 in HasB, is poorly conserved (with an identity of two out of seven). These differences might be responsible for the specificity of HasB toward HasR.
The genetic association of hasB with the gene encoding its dedicated TBDT receptor HasR in the has operon enables their coregulated expression. HasB is therefore positively regulated by the signaling cascade and is thus produced at a higher level when a heme-loaded hemophore is available. Such a high HasB level might be required for heme-hemophore uptake. Since HasB is specific to HasR, it might either not energize other TBDT receptors or not interact with them, preventing wasting of energy or a loss of the HasB molecular pool. We have previously shown that hemophore-dependent heme uptake in E. coli expressing the Has system is a high-energy-consuming process. Whereas free heme uptake via HasR functions at basal TonB-ExbB-ExbD levels, full TonB-ExbB-ExbD expression is required for recycling empty hemophore from the cell surfaces (16). HasB6 efficiently substitutes for TonB in this process (S. Létoffé, unpublished data). Thus, we hypothesize that TonB has only weak activity toward HasR, either because of low affinity or because of an incomplete interaction. HasB is the only described case of a TonB protein specific for only one TBDT receptor. However, the rapidly increasing DNA sequence data for microbial genomes frequently show the presence of potential TonB homologs in the vicinity of TBDT receptors, suggesting that the existence of TonB-TBDT receptor-specific pairs might not be an exception. In the case of the Has system, TonB can be considered a poor energy transmitter, allowing a basal function for the Has system, which works fully only in the presence of its own specific TonB ortholog, HasB.
We thank Sylvie Létoffé and Philippe Delepelaire for helpful practical and conceptual discussions.
Published ahead of print on 19 October 2007. ![]()
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