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Journal of Bacteriology, March 2008, p. 1866-1870, Vol. 190, No. 6
0021-9193/08/$08.00+0 doi:10.1128/JB.01636-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Unité des Membranes Bactériennes, Département de Microbiologie, Institut Pasteur, CNRS URA 2172, 75724 Paris Cedex 15, France
Received 9 October 2007/ Accepted 23 December 2007
| ABSTRACT |
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-aminolevulinic (ALA) transport through the E. coli inner membrane. We show here that hemTUV genes complement the Dpp permease for heme utilization as an iron source and thus are functional in E. coli. However, hemTUV genes do not complement the Dpp permease for ALA uptake, indicating that the HemTUV permease does not transport ALA. Peptides do not inhibit heme uptake in vivo, indicating that, unlike Dpp permease, HemTUV permease does not transport peptides. HemT, the periplasmic binding protein, binds heme. Heme binding is saturable and not inhibited by peptides that inhibit heme uptake by the Dpp system. Thus, the S. marcescens HemTUV permease and, most likely, HemTUV orthologs present in many gram-negative pathogens form a class of heme-specific permeases different from the Dpp peptide/heme permease characterized in E. coli. | INTRODUCTION |
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In many gram-negative pathogens, heme permeases have similar sequences and organizations and are comprised of one periplasmic heme binding protein, HemT, one transmembrane protein, HemU, and one ABC protein, HemV (21). Heme permease structural genes are usually clustered, and only one copy is present in each bacterial genome. The heme permease gene set is localized in an iron-regulated operon that often also includes a gene encoding one heme outer membrane receptor (26).
Pathogenic Escherichia coli strains have genes that are homologous to hemTUV and are linked to the structural gene for the heme outer membrane receptor. This cluster has a similar genetic organization and chromosome localization in many E. coli strains, suggesting that it was acquired by horizontal transfer (28).
On the other hand, E. coli K-12 lacks a heme outer membrane receptor and heme permease orthologs and is unable to use exogenously added heme as an iron source. Nevertheless, a recombinant clone expressing only a foreign heme outer membrane receptor, such as ShuA, HemR, or HasR, can use heme as an iron source, suggesting that there is an unidentified heme permease. In previous work, we showed that E. coli heme permease consists of the dipeptide ABC transporter DppBCDF functioning with one of two optional periplasmic binding proteins, either MppA, the L-alanyl-
-D-glutamyl-meso-diaminopimelate binding protein (14), or DppA, the dipeptide binding protein (1). Purified DppA and MppA proteins are able to bind heme in vitro with binding constants of approximately 10 and 50 µM, respectively. Peptides compete for heme binding to DppA and MppA in vitro, while in vivo they inhibit heme transport (9). The DppA/MppA DppBCDF permease also transports
-aminolevulinic acid (ALA), a heme precursor that resembles the GG dipeptide (25).
Two other periplasmic DppA homologs, the E. coli NikA protein and Haemophilus influenzae HbpA, also bind heme (18) (5). While periplasmic binding proteins are usually specific for one substrate or closely related structural homologs, it is surprising that NikA, DppA, and MppA bind heme in addition to their cognate substrates. However, it is not known whether HbpA and NikA also bind peptides in addition to heme.
The present work was undertaken to determine whether other heme binding periplasmic proteins can bind peptides. The hemTUV genes of S. marcescens were cloned and expressed in an E. coli recombinant strain having a heme outer membrane receptor enabling heme uptake through the outer membrane and carrying a dppF::Km mutation which inactivated the Dpp-heme permease.
| MATERIALS AND METHODS |
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lacU169 rpsL relA thi) and POP3 hemA were obtained from a laboratory collection. FB827 dppF::Tn5 has been described previously (9). S. marcescens DB11 was described by Kurz et al. (7) and was a gift from J. Ewbank. Mutations were introduced into strains by phage P1 transduction. pAM 238 and pTRC99 were obtained from a laboratory collection, and pAM 238-hasR has been described previously (8). pTRC99-hemTUV and pTRC99-hemT are described in this paper.
Media and growth conditions. Hemin, bovine hemoglobin, ALA, 2,2'dipyridyl (Dip), and isopropyl-β-D-thiogalactopyranoside (IPTG) were obtained from Sigma Chemical Company (Lyon, France). The hemoglobin concentration was calculated on the basis of the heme monomer. Hemoglobin and ALA solutions were sterilized by passage through 0.45-µm-pore-size filters. Hemin was dissolved immediately before use in a minimal volume of 0.1 N NaOH, filtered, and diluted with the appropriate buffer to obtain the desired concentration. Bacteria were grown aerobically at 37°C in LB rich medium, in M63, or in M63 without added iron salt (M63*). All minimal media were supplemented with 0.4% glucose. When required, Dip was added at a final concentration of 60 µM to M63*. IPTG (1 mM) was added to induce the pTRC99 trc promoter. Antibiotics were added at the following final concentrations: ampicillin, 50 µg ml–1; kanamycin, 25 µg ml–1; spectinomycin, 50 µg ml–1; tetracycline, 10 µg ml–1; and chloramphenicol, 15 µg ml–1. For each strain, the carbon source and the appropriate antibiotics were added to solid and liquid media (data not shown). All cultures were grown with aeration at 37°C, and the optical density at 600 nm (OD600) was determined.
Growth promotion assays. Cultures of strain FB827(pAM 238-hasR) carrying various mutations and plasmids were grown in M63 containing glucose to an OD600 of 1, and 100-µl aliquots were mixed with 3.5 ml of M63* soft agar (0.7% agar) and poured onto M63* plates containing Dip supplemented with 1 mM IPTG to induce the pTRC99-encoded genes. Aliquots (50 µl) of bovine hemoglobin at various concentrations were placed in wells punched in the solidified agar. The plates were incubated overnight at 37°C, and the radius of the growth halo around each well was measured. All experiments were repeated three times.
To test its ability to use ALA, heme auxotroph strain POP3 hemA carrying various mutations and plasmids was streaked on M63 plates containing the appropriate antibiotics and supplemented with either 0.5 or 5 µg/ml of ALA. Colony sizes were measured after 48 h of incubation at 37°C.
Genetic techniques. Preparation of P1 lysates and transduction were performed as described by Miller (11). Competent cells were prepared by the calcium chloride method.
Extraction and manipulation of plasmids. Standard methods were used for isolation of plasmid DNA, cloning, restriction enzyme analysis, and transformation.
Plasmid construction. Plasmids encoding HemTUV and HemT were constructed by amplification of S. marcescens DB11 genomic DNA using complementary oligonucleotides (sequences available upon request). Amplified fragments with appropriate restriction nuclease recognition sites were inserted into pTRC99. Amplified gene sequences were checked by DNA sequencing.
Production and purification of HemT protein. HemT was purified by using the procedure used to purify DppA and MppA described previously (9). Briefly, 6 liters of a POP3(pTRC99-HemT) cell culture was grown at 37°C in M63. When the culture reached an OD600 of 0.2, IPTG was added to a final concentration of 1 mM. The culture was grown for an additional 4 h at 37°C to an OD600 of 0.8 and harvested by centrifugation for 15 min at 8,000 x g at 4°C. The cell pellet was washed once in TE buffer (10 mM Tris-HCl [pH 7.5], 1 mM EDTA), resuspended at room temperature in 480 ml of 30% (wt/vol) sucrose (OD600, 10), and incubated for 30 min at room temperature. Then EDTA (pH 8) was added to a final concentration of 10 mM, and cells were incubated again for 15 min at room temperature. The cell suspension was centrifuged at 10,000 x g for 30 min at 4°C. The supernatant containing the periplasmic shock fluid was concentrated by 80% ammonium sulfate precipitation and then extensively dialyzed against 50 mM Tris-HCl (pH 7.5)-80 mM NaCl at 4°C.
Samples of concentrated osmotic shock fluid were first purified by cation-exchange chromatography performed as described previously for DppA (9). This was followed by anion-exchange chromatography using gels preequilibrated with 20 mM Tris-HCl (pH 8.5). Elution was performed with 20 mM Tris-HCl (pH 8.5)-1 M NaCl. Fractions were collected, and their HemT contents and purity were evaluated by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). Fractions containing pure HemT that produced a single protein band at an apparent molecular mass of 27 kDa were pooled and concentrated by using an Amicon Ultra 15 with a 10,000-molecular-weight cutoff (Millipore). The N-terminal amino acid sequence was determined by the Plateforme d'Analyze et de Microséquence des Protéines of the Institut Pasteur.
Nondenaturing PAGE and detection of heme by chemiluminescence. Aliquots (30 µl) of purified HemT (concentration, 3 x 10–6 M) were incubated at room temperature for 30 min with heme at various concentrations, including 10–4, 10–5, 10–6, and 10–7 M. Heme-loaded samples were separated by PAGE (at 4°C in the absence of SDS), and the proteins were transferred to nitrocellulose filters. Heme complexed with protein bands on the gel retained its intrinsic peroxidase activity, which was detected by chemiluminescence (ECL Plus; Amersham) as described previously (24). The signal was measured either by autoradiography on film or with a Storm Imager.
Peptide inhibition of heme binding to HemT was tested by adding to 30-µl purified HemT aliquots (concentration, 3 x 10–6 M) either heme alone (10–4 M) or a mixture of heme (10–4 M) and peptides Ala-Ala (AA) and Pro-Phe-Lys (PFK) (10–4 M each). Peptone and tryptone inhibition of heme binding to HemT was also tested by adding to 10-µl purified HemT aliquots (concentration, 3 x 10–6 M) a mixture of heme (10–4 M), peptone (final concentration, 7%), and tryptone (final concentration, 7%). The mixtures were separated by PAGE, and heme was detected as described above.
| RESULTS |
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The DB11 hemTUV genes were amplified by PCR and cloned into pTRC99. Strain FB827(pAM 238-hasR) and the isogenic mutant FB827 dppF::Km(pAM 238-hasR) were transformed with pTRC99-dppABCDF or pTRC99-hemTUV. Strains were grown in M63 to an OD600 of 1 and tested for growth on M63* plates containing Dip and 1 mM IPTG. Because of iron restriction, none of the tested strains could grow on these plates. Wells were punched into solidified agar and filled with 50 µl of bovine hemoglobin at concentrations ranging from 1 to 50 µM. As shown previously by another growth promotion assay (9), FB827(pAM 238-hasR) could grow only around hemoglobin-containing wells; the lowest hemoglobin concentration that resulted in a significant halo was 5 µM, and neither strain FB827(pAM 238) lacking heme outer membrane receptor HasR nor mutant FB827 dppF::Km(pAM 238-hasR) could grow on these plates around the wells containing hemoglobin at concentrations up to 50 µM (hemoglobin concentrations equal to or higher than 100 µM could not be used as they might promote nonspecific growth in this test). FB827 dppF::Km(pAM 238-hasR)(pTRC99-dppABCDF) grew as well as parental strain FB827(pAM 238-hasR) around the hemoglobin-filled wells (Table 1).
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Peptides do not inhibit iron heme utilization via HemTUV permease. The dipeptide AA has a strong affinity for DppA (19), and the tripeptide PFK is transported by MppA-OppBCDF permease (14). In previous work we showed that a combination of these two peptides inhibits heme utilization via the Dpp permease (9). We thus tested whether such competition also occurs via the HemTUV permease. Strains FB827 dppF::Km(pAM 238-hasR)(pTRC99-dppABCDF) and FB827 dppF::Km(pAM238-hasR)(pTRC99-hemTUV) were grown and tested as described above on M63* plates containing Dip and 1 mM IPTG with wells filled with either 50 µM hemoglobin alone or a mixture of hemoglobin and various peptides, as indicated in Table 2. Growth of FB827 dppF::Km(pAM 238-hasR)(pTRC99-dppABCDF), which has a functional Dpp permease, was inhibited around wells containing a mixture of hemoglobin and either peptone (20%) or tryptone (20%) or containing a combination of the dipeptide AA and the tripeptide PFK (100 µM each). However, the growth of FB827 dppF::Km(pAM 238-hasR)(pTRC99-hemTUV) was the same in all wells independent of the presence of peptides, indicating that none of the peptides inhibited iron heme utilization via HemTUV (Table 2).
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HemT overproduction does not inhibit ALA transport. To determine whether HemT sequesters heme or inhibits the Dpp permease, we tested the effect of HemT overproduction on the ability of organisms to use ALA at low concentrations. POP3 hemA(pTRC99-hemT) grew as well as POP3 hemA on M63 plates containing glucose and 1 mM IPTG supplemented with 0.5 µg/ml of ALA (Table 3). Thus, HemT does not bind ALA and does not inhibit Dpp permease. It might withhold heme from Dpp permease.
HemT "in vitro" properties. POP3(pTRC99-hemT) was grown in M63 with 1 mM IPTG to induce the hemT gene and was osmotically shocked to release its periplasmic contents. A protein band induced by IPTG and with an apparent molecular mass of 27 kDa was detected in the shock fluid (Fig. 1A, lane 1). The N-terminal sequence of the HemT protein was AQRIVS, indicating that the hemT gene encodes a 23-residue, cleavable, N-terminal signal peptide. This signal peptide had a twin-arginine motif and an overall sequence similar to a Tat signal sequence (17). We thus tested whether HemT is translocated to the periplasm by the Tat system, which delivers folded proteins. The HemT amounts in the periplasm were similar in tat+ and tat backgrounds, indicating that HemT translocation is Tat independent (data not shown). HemT was purified as described in Materials and Methods. This resulted in a single band on SDS-PAGE gels at an apparent molecular mass of 27 kDa (Fig. 1 A, lane 2). Pure HemT was incubated with 10–4 M heme and electrophoresed on a nondenaturing PAGE gel, which allowed separation of free heme, apoprotein, and heme-loaded protein without dissociation of heme from the protein. Heme bound to the protein was detected by chemiluminescence (Fig. 1 B, lanes 1 and 3). HemT was incubated with various concentrations of heme. The samples were analyzed as described above, and the heme bound to proteins was determined by enhanced chemoluminescence. Heme binding was saturable with a dissociation constant for heme less than 10–6 M (data not shown).
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| DISCUSSION |
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The contribution of each type of permease to heme acquisition by bacterial pathogens is actually not known. BLAST searches for putative heme permeases did not reveal any hemTUV orthologs in several species, such as Neisseria and Haemophilus species, which have functional heme outer membrane receptors and which are able to use heme as an iron source (15). It is tempting to speculate that in these organisms heme is taken up by peptide permeases. In addition, hemTUV gene inactivation in various mutants, such as Y. enterocolitica, Yersinia pestis, and Vibrio cholerae mutants, does not abolish heme uptake, suggesting that in these mutants peptide permeases may take over from the HemTUV permeases (13, 20, 22). Genetic inactivation of each permease and of both types of permeases in these strains should help elucidate the relative role of each type of permease in heme uptake.
A priori, heme transport through the inner membrane by E. coli K-12, an organism lacking an outer membrane heme receptor, seems meaningless. However, it is likely that the peptide/heme permease is involved in endogenous heme recycling.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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Published ahead of print on 4 January 2008. ![]()
| REFERENCES |
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-D-glutamyl-meso-diaminopimelate. J. Bacteriol. 180:1215-1223.
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