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Biochemistry 2007, 46, 12198-12211
Biochemical and Structural Characterization of Pseudomonas aeruginosa Bfd and FPR: Ferredoxin NADP+ Reductase and Not Ferredoxin Is the Redox Partner of Heme Oxygenase under Iron-Starvation Conditions†,‡ An Wang,§ Yuhong Zeng,§ Huijong Han,| Saroja Weeratunga,§ Bailey N. Morgan,§ Pierre Moe¨nne-Loccoz,⊥ Ernst Scho¨nbrunn,| and Mario Rivera*,§ Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, UniVersity of Kansas, Multidisciplinary Research Building, 2030 Becker DriVe, Room 220 E, Lawrence, Kansas 66047, Department of Medicinal Chemistry, 1251 Wescoe Hall DriVe, UniVersity of Kansas, Lawrence, Kansas 66045, and Department of EnVironmental and Biomolecular Systems, OGI School of Science and Engineering at Oregon Health and Science UniVersity, BeaVerton, Oregon 97006-8921 ReceiVed July 3, 2007; ReVised Manuscript ReceiVed August 24, 2007
ABSTRACT: Among the 118 genes upregulated by Pseudomonas aeruginosa in response to iron starvation [Ochsner, U. A., Wilderman, P. J., Vasil, A. I., and Vasil, M. L. (2002) Mol. Microbiol. 45, 1277-1287], we focused on the products of the two genes encoding electron transfer proteins, as a means of identifying the redox partners of the heme oxygenase (pa-HO) expressed under low-iron stress conditions. Biochemical and spectroscopic investigations demonstrated that the bfd gene encodes a 73-amino acid protein (paBfd) that incorporates a [2Fe-2S]2+/+ center, whereas the fpr gene encodes a 258-residue NADPH-dependent ferredoxin reductase (pa-FPR) that utilizes FAD as a cofactor. In vitro reconstitution of pa-HO catalytic activity with the newly characterized proteins led to the surprising observation that pa-FPR efficiently supports the catalytic cycle of pa-HO, without the need of a ferredoxin. In comparison, electron transfer from pa-Bfd to pa-HO is sluggish, which strongly argues against the possibility that the seven electrons needed by pa-HO to degrade biliverdin are transferred from NADPH to pa-HO in a ferredoxin (Bfd)dependent manner. Given that pa-HO functions to release iron from exogenous heme acquired under iron-starvation conditions, the use of a flavoenzyme rather than an iron-sulfur center-containing protein to support heme degradation is an efficient use of resources in the cell. The crystal structure of pa-FPR (1.6 Å resolution) showed that its fold is comparable that of the superfamily of ferredoxin reductases and most similar to the structure of Azotobacter Vinelandii FPR and Escherichia coli flavodoxin reductase. The latter two enzymes interact with distinct redox partners, a ferredoxin and a flavodoxin, respectively. Hence, findings reported herein extend the range of redox partners recognized by the fold of pa-FPR to include a heme oxygenase (pa-HO).
Pathogenic bacteria need iron to colonize (infect) an organism. However, the concentration of free iron in mammals is typically very low (∼10-9 M) because it is sequestered by iron-binding and iron-containing compounds such as transferrin, lactoferrin, heme, hemoglobin, and ferritin (1). In addition, mammals have evolved means of fighting invading pathogens by making iron even less accessible by † This work was supported by grants from the National Institutes of Health (GM-50503, M.R.) and the National Science Foundation (MCB0446326, M.R.) and by the Center for Environmental Beneficial Catalysis, University of Kansas, under National Science Foundation Grant (EEC-0310689). ‡ Coordinates for the structure of pa-FPR have been deposited in the Protein Data Bank as entry 2QDX. * To whom correspondence should be addressed: Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, Multidisciplinary Research Building, 2030 Becker Dr., Room 220 E, Lawrence, KS 66047. Phone: (785) 864-4936. Fax: (785) 864-5396. E-mail:
[email protected]. § Ralph N. Adams Institute for Bioanalytical Chemistry & Department of Chemistry, University of Kansas. | Department of Medicinal Chemistry, University of Kansas. ⊥ OGI School of Science and Engineering at Oregon Health and Science University.
reducing levels of transferrin and by downregulating the recycling of iron from macrophages (2). It has also been shown that lipocalin 2, an iron-binding protein innate to the immune response, sequesters iron from bacterial siderophores in the early stages of bacterial infection (3). It is therefore not surprising that pathogens such as Neisseriae meningitidis, Haemophilus influenzae, Shigella dysenteriae, Vibrio cholerae, and the opportunistic Pseudomonas aeruginosa have evolved sophisticated mechanisms for iron acquisition, including the utilization of heme iron (4, 5). Heme-containing proteins and in particular hemoglobin constitute an important reservoir of iron given that more than two-thirds of the total iron is chelated by heme and that ∼95% of iron-bound heme is in the form of hemoglobin (6). Consequently, many pathogenic bacteria have evolved specific heme uptake systems for acquiring heme iron from mammalian hosts. Although these systems are best understood in Gram-negative bacteria (4, 5), it has been recently shown that Staphylococcus aureus not only uses heme as an iron source but also prefers heme iron in the initial stages of infection (7). Heme uptake and utilization is also a mechanism used by the
10.1021/bi7013135 CCC: $37.00 © 2007 American Chemical Society Published on Web 10/04/2007
pa-FPR Is the Redox Partner of pa-HO
Biochemistry, Vol. 46, No. 43, 2007 12199
FIGURE 1: Schematic representation of the heme oxygenase catalytic cycle. Emphasis has been placed on the input of the first two electrons that are utilized by the enzyme to reduce coordinated O2 at the active site. The resultant ferric hydroperoxide intermediate (FeIII-OOH) reacts with the macrocycle to form meso-hydroxyheme, which in the presence of O2 and five additional reducing equivalents is converted to biliverdin and free iron.
opportunistic pathogen P. aeruginosa, which can deploy two operons regulated by Fur, the master Fe uptake regulator (8). The global iron response associated with Fur-regulated genes includes the heme uptake systems phu (Pseudomonas heme uptake) and has (heme acquisition system). The phu locus consists of a receptor gene (phuR) and the phuSTUVW operon encoding a typical ABC transporter. The second uptake system, has, consists of a heme receptor (hasR) and a protein that binds heme with high affinity, also known as a hemophore (4). Once internalized to the cytoplasm, heme is delivered to a heme oxygenase (pa-HO)1 for its degradation to biliverdin, thus facilitating release of the heme iron for subsequent metabolic use (9). Release of heme iron is accomplished by the breakdown of heme to biliverdin. This is a complex reaction requiring the input of seven electrons and three molecules of O2, which must be delivered to HO rapidly and efficiently to sustain catalytic activity (Figure 1). Heme breakdown starts with the one-electron reduction of ferric HO (resting state) to the deoxyferrous state, followed by the rapid binding of dioxygen to form an oxyferrous complex (FeII-O2) (10). Injection of a second electron into the FeII-O2 complex triggers electron rearrangement that leads to the formation of a ferric peroxide (FeIII-OO-) complex, which accepts a proton to form a ferric hydroperoxide (FeIII-OOH) oxidizing species (11). Ring oxidation involves attack of the FeIII-OOH intermediate on the aromatic macrocycle (12) which forms a meso-hydroxyheme intermediate, which undergoes a subsequent O2- and electron-dependent elimination of the hydroxylated meso carbon as CO, thus forming verdoheme. Verdoheme is then oxidized to the FeIII-biliverdin complex in a reaction that requires both O2 and additional electrons (13, 14). The FeIIIbiliverdin complex must be reduced to the FeII-biliverdin complex prior to the sequential release of FeII and biliverdin (15). 1 Abbreviations: AV-FPR, Azotobacter Vinelandii ferredoxin reductase; bfd, bacterioferritin-associated ferredoxin; bfr, bacterioferritin; CpFd, Clostridium pasteurianum ferredoxin; DTT, dithiothreitol; EcFldR, Escherichia coli flavodoxin reductase; EPR, electron paramagnetic resonance; FAD, flavin adenine dinucleotide; NAD(P)H, nicotinamide adenine dinucleotide (phosphate); FNR, ferredoxin NAD(P)H reductase; HO, heme oxygenase; IPTG, isopropyl 1-thiol-D-galactopyranoside; MS, mass spectrometry; pa-FPR, Pseudomonas aeruginosa ferredoxin reductase; pa-HO, P. aeruginosa heme oxygenase; PMSF, phenylmethanesulfonyl fluoride.
The identification and characterization of redox partners that deliver electrons to HO, as well as the characterization of protein-protein interactions that facilitate the vectorial electron flow from NAD(P)H to HO, are important steps toward a molecular-level understanding of heme metabolism. Cytochrome P450 reductase supports the catalytic activity of mammalian HO-1 and HO-2 by donating all seven electrons (15). In comparison, our current understanding regarding the nature of the redox partner(s) that supports the catalytic activity of bacterial HO enzymes is significantly less developed. It is thought that cyanobacterial and eubacterial HOs are ferredoxin-dependent. It is noteworthy, however, that reports proposing this idea also state that HO activity in cell extracts containing reduced ferredoxin also requires the presence of a second (auxiliary) reductant, such as trolox or ascorbate (16-19). In fact, in the absence of such auxiliary reducing agents, HO activity is very slow (16, 18) or is arrested at the oxyferrous heme stage (17). It is also important to note that despite the widespread belief that bacterial HOs are ferredoxin-dependent the specific ferredoxins that support the activity of these HO enzymes are not yet known. We have recently observed a potentially important clue regarding the nature of the enzymes that transfer electrons to pa-HO under conditions of iron starvation. This indication comes from the analysis of relatively recently published data on genes affected by the ironstarvation response in P. aeruginosa (20), which revealed that the level of expression of 118 genes was increased at least 3-fold under iron-starvation conditions relative to ironreplete conditions. We noticed that among the 118 upregulated genes, the level of expression of a gene encoding a ferredoxin (bfd) is increased 203-fold and that of a gene encoding a ferredoxin reductase (fpr) 3-fold. These observations suggested to us that the ferredoxin encoded by the bfd gene may be the physiological reductant of pa-HO, a hypothesis that is in agreement with the fact that among the 118 genes upregulated by iron limitation, the level of expression of the gene encoding pa-HO (pigA, or PA0672) is also increased 138-fold and that there is no other upregulated gene encoding a ferredoxin or other classical electron transfer protein. Moreover, the product of the fpr gene, a ferredoxin reductase (pa-FPR), is likely the enzyme that transfers electrons to pa-Bfd from NAD(P)H. Hence, the motivation for these studies was to probe a hypothesis
12200 Biochemistry, Vol. 46, No. 43, 2007 that the seven electrons needed by pa-HO to degrade heme and release iron in the cytosol of P. aeruginosa are shuttled from NAD(P)H to pa-FPR and subsequently to pa-Bfd, which in turn delivers them to pa-HO. These investigations uncovered the surprising finding that pa-FPR efficiently sustains the catalytic activity of pa-HO in vitro, whereas the ferredoxin (pa-Bfd) is extremely inefficient at transferring electrons to the oxygenase. These observations strongly suggest that the flavoenzyme pa-FPR is the physiological electron donor to pa-HO, a situation that is similar that observed with mammalian HOs, which are reduced by the flavoprotein cytochrome P450 reductase. EXPERIMENTAL PROCEDURES Cloning and Expression of pa-Bfd and pa-FPR. The genes encoding pa-Bfd (PA3530) and pa-FPR (PA3397) were synthesized and subcloned into the pET11a vector (GeneScript Corp., Piscataway, NJ). The genes were engineered with silent mutations introducing codons favored by Escherichia coli (21) and with NdeI and BamHI restriction enzyme sites at the 5′ and 3′ ends, respectively, for subcloning into the pET11a vector (Figures S1 and S2 of the Supporting Information). The pET11a vector harboring the bfd gene was then transformed into E. coli BL21(DE3) Gold cells (Stratagene) for protein expression, whereas that containing the fpr gene was transformed into E. coli ArcticExpress RIL Competent Cells (Stratagene), to overcome protein misfolding and insolubility issues observed with BL21(DE3) Gold cells. To express pa-Bfd, a single colony of E. coli BL21(DE3) Gold cells was cultured overnight in 5 mL of LB medium containing 100 µg/mL ampicillin; the cells were subsequently subcultured in 1 L of fresh LB/ ampicillin medium and grown at 37 °C until the OD at 600 nm reached 0.5-0.6. Protein expression was then induced by addition of isopropyl 1-thiol-D-galactopyranose (IPTG) to a final concentration of 1 mM, and the cells were cultured for an additional 5 h at 30 °C, before they were harvested by centrifugation (4000 rpm for 10 min) and stored at -20 °C. To express pa-FPR, a single colony of ArcticExpress RIL cells was introduced into 10 mL of LB medium containing ampicillin as described above and cultured at 37 °C and 220 rpm overnight. The cell suspension was transferred into 1 L of LB/ampicillin medium and further cultured at 37 °C (4-5 h) to an OD of approximately 0.7. At this point, the cells were transferred to another shaker incubator (Barnstead) pre-equilibrated at 10 °C and cultured for an additional 30 min. Protein expression was then induced by addition of IPTG to a final concentration of 0.3 mM, and the cells were subsequently cultured for approximately 14 h before they were harvested by centrifugation (4000 rpm for 10 min) and stored at - 20 °C. Purification and Reconstitution of the Iron-Sulfur Cluster in pa-Bfd. One gram of harvested cells was resuspended in 3 mL of lysis buffer [50 mM Tris-HCl (pH 8.0 and 4 °C), 1 mM EDTA, and 100 mM NaCl]. Lysozyme (0.5 mg/mL), PMSF (0.5 mM), and deoxycholic acid (1.3 mg/mL) were added to the cell suspension, followed by stirring at 4 °C for 20 min. Mg2+ (final concentration of 4.2 mM) and DNase I (Sigma-Aldrich, St. Louis, MO) were added to the lysate before it was incubated at 37 °C for 30 min. The cell suspension was further incubated at room temperature with stirring for 60 min, followed by centrifugation for 2 h at
Wang et al. 23 500 rpm and 4 °C. The pellet was resuspended in 50 mM potassium phosphate buffer (pH 7.0) containing 6 M urea and stirred at room temperature for 60 min. The suspension was centrifuged at 23 500 rpm for 1.5 h; the supernatant containing denatured pa-Bfd was placed on an ice bath and bubbled with argon for ∼30 min, followed by addition of DTT (dithiothreitol) to a final concentration of 100 mM, and bubbled with Ar for an additional 15 min. The solution was then diluted 10 times by transferring it into 50 mM potassium phosphate buffer, previously degassed by being bubbled with Ar for 45 min, via a cannula. This was followed by slow addition of previously degassed solutions of FeSO4‚7H2O and Na2S (200 mM each) to a final concentration of 1.0 mM and incubation with continuous stirring under an argon atmosphere. The resultant solution was subsequently mixed with a suspension of Q-Sepharose resin under a laboratory atmosphere; the resin was allowed to settle, the supernatant discarded, and the resin washed three times, each with 60 mL of 600 mM NaCl in 50 mM potassium phosphate buffer (pH 7.0). The solutions from each of the three washes were combined and dialyzed against 4 L of 50 mM potassium phosphate buffer (pH 7.0) for 3 h before the mixture was loaded onto a column packed with Q-Sepharose [12 cm × 2.5 cm (inside diameter)] pre-equilibrated with the same buffer used for dialysis. The protein was eluted with 50 mM potassium phosphate buffer (pH 7.0) with a salt gradient from 0 to 300 mM NaCl. Fractions containing pa-Bfd were pooled together, concentrated, and loaded onto a Sephadex G-50 column [55 cm × 1.5 cm (inside diameter)], which was eluted with previously degassed 50 mM potassium phosphate (pH 7.0) containing 100 mM NaCl. Fractions with an absorbance ratio (A424/A280) larger than 0.5 were pooled, and the resultant solution was concentrated by ultrafiltration and then degassed with argon before being stored at -80 °C. Characterization of the Fe-S Cluster in pa-Bfd. The purity of overexpressed pa-Bfd was analyzed using SDS-PAGE (18% polyacrylamide) and electrospray ionization mass spectrometry; the latter was performed in the Mass Spectrometry Laboratory at the University of Kansas. Molar extinction coefficients of pa-Bfd were determined by amino acid analysis at the Molecular Structure, Sequencing and Synthesis Facility, Michigan State University (East Lansing, MI). The electronic absorption spectra of pa-Bfd were recorded in 50 mM potassium phosphate buffer (pH 7.0) using a UV-vis S2000 spectrophotometer (Ocean Optics, Dunedin, FL). The protein concentration for the EPR and resonance Raman experiment was ∼1.3 mM in 50 mM HEPES (pH 7) containing 100 mM NaCl and ∼2 mM DTT. EPR spectra of oxidized and reduced pa-Bfd were obtained on a Bruker E500 X-band EPR spectrometer equipped with a superX microwave bridge and a dual-mode cavity with a helium flow cryostat (ESR900, Oxford Instruments, Inc.). The same EPR samples were used for the resonance Raman (RR) characterization using a custom Dewar and cold finger to keep the sample temperature at 100 K. The 488 nm excitation (50 mW) of an Innova 90 argon laser (Coherent, Santa Clara, CA) was focused on the sample with a cylindrical lens. The back-scattered light was collected with a camera lens and focused on the entrance slit of a custom McPherson 2061/207 spectrograph (0.67 m with 2400 groove grating) equipped with a Princeton Instruments liquid N2cooled CCD detector (LN-1100PB). A Kaiser Optical
pa-FPR Is the Redox Partner of pa-HO supernotch filter was used to attenuate the Rayleigh scattering. Frequencies were calibrated relative to aspirin and are accurate to (1 cm-1. Purification of pa-FPR. Cells were resuspended in 3 mL of lysis buffer, stirred for 20 min at 4 °C, incubated at 37 °C for 20 min, stirred at ambient temperature for 1 h, and then sonicated at 4 °C. The lysed cells were centrifuged at 35 000 rpm for 2 h to sediment cell debris, and the supernatant was dialyzed against 4 L of 20 mM Tris-HCl (pH 7.5, 4 °C) with at least three buffer changes over a period of approximately 16 h. The resultant solution was applied to a Q-Sepharose Fast Flow column [10 cm × 2.5 cm (inside diameter)] previously equilibrated with 20 mM Tris-HCl (pH 7.5, 4 °C). The column was washed with 3 volumes of 20 mM Tris-HCl (pH 7.5) containing 50 mM NaCl, and the protein eluted in the same buffer with a linear gradient (from 50 to 500 mM) of NaCl. Fractions containing FPR (yellow) were pooled, concentrated, and then loaded onto a Sephadex G-50 column (3.0 cm × 100 cm) pre-equilibrated and eluted with phosphate buffer (µ ) 0.1, pH 7.0) at 4 °C. Fractions with an A280/A450 absorbance ratio of
