Báo cáo khoa học: Heme binding to the second, lower-affinity site of the global iron regulator Irr from Rhizobium leguminosarum promotes oligomerization potx

Heme binding to the second, lower-affinity site of the global iron regulator Irr from Rhizobium leguminosarum promotes oligomerization Gaye F. White 1,2 , Chloe Singleton 1 , Jonathan D. Todd 2 , Myles R. Cheesman 1 , Andrew W. B. Johnston 2 and Nick E. Le Brun 1 1 School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich, UK 2 School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK Introduction Iron is essential for almost all forms of life, fulfilling functions ranging from respiration to DNA synthesis. The metal occurs in cells as a protein cofactor in dif- ferent forms: as the bare metal or, more commonly, in heme and iron-sulfur clusters. Despite its abundance in the biosphere, iron has poor bioavailability owing to its propensity, in the presence of oxygen and water, to form insoluble ferric oxy–hydroxide complexes [1], such that cells of all types employ complex mecha- nisms to recruit it from the environment. In addition, Keywords a-proteobacteria; fur; heme; iron; transcriptional regulation Correspondence N. E. Le Brun, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK Fax: +44 1603 592003 Tel: +44 1603 592699 E-mail: n.le-brun@uea.ac.uk (Received 3 February 2011, revised 17 March 2011, accepted 1 April 2011) doi:10.1111/j.1742-4658.2011.08117.x The iron responsive regulator Irr is found in a wide range of a-proteobac- teria, where it regulates many genes in response to the essential but toxic metal iron. Unlike Fur, the transcriptional regulator that is used for iron homeostasis by almost all other bacterial lineages, Irr does not sense Fe 2+ directly, but, rather, interacts with a physiologically important form of iron, namely heme. Recent studies of Irr from the N 2 -fixing symbiont Rhizobium leguminosarum (Irr Rl ) showed that it binds heme with submi- cromolar affinity at a His-Xxx-His (HxH) motif. This caused the protein to dissociate from its cognate DNA regulatory iron control element box sequences, thus allowing expression of its target genes under iron-replete conditions. In the present study, we report new insights into the mecha- nisms and consequences of heme binding to Irr. In addition to the HxH motif, Irr binds heme at a second, lower-affinity site. Spectroscopic studies of wild-type Irr and His variants show that His46 and probably His66 are involved in coordinating heme in a low-spin state at this second site. By contrast to the well-studied Irr from Bradyrhizobium japonicum, neither heme site of Irr Rl stabilizes ferrous heme. Furthermore, we show that heme-free Irr Rl exists as a mixture of dimeric and larger, likely hexameric, forms and that heme binding promotes Irr Rl oligomerization. Bioanalytical studies of Irr Rl variants showed that this property is not dependent on the HxH motif but is associated with heme binding at the second site. Structured digital abstract l Irr binds to irr by molecular sieving (View Interaction 1, 2) l Irr binds to irr by cosedimentation in solution (View interaction) Abbreviations EPR, electron paramagnetic resonance; HRM, heme regulatory motif; ICE, iron control element. FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS 2011 the very properties that make iron essential also make it toxic in oversupply, such that the amount and form of iron in the cell must be carefully regulated [1,2]. In bacteria, several different iron regulatory systems are now known. The best studied are the functionally and structurally similar, but evolutionarily unrelated global regulators, Fur and DtxR. Under iron-sufficient conditions, both of these bind Fe 2+ , causing a confor- mational change that increases the affinity of the pro- tein for operator sequences located 5¢ of the regulated genes, resulting (usually) in transcriptional repression [3,4]. When iron is scarce, Fe 2+ dissociates, releasing the protein from DNA, thereby switching on genes involved in, for example, iron recruitment and uptake. The subphylum a-proteobacteria contains important pathogens of animals (e.g. Brucella, Rickettsia) and plants (Agrobacterium), symbionts (the N 2 -fixing rhizo- bia), many of the most abundant bacteria in the oceans (the Roseobacters and the SAR11 clade, includ- ing Pelagibacter) and some laboratory model organ- isms (e.g. Paracoccus, Rhodobacter), as well as being the source of mitochondria. The relatively few studies on iron-responsive gene regulation in members of this important group have shown that these bacteria are very different from those that use the Fur regulator. Although many a-proteobacteria contain a Fur homo- logue [5], in those cases where this gene product was studied directly, it was shown to have a minor regula- tory role, repressing a few genes in response to manga- nese (and not iron) availability; hence, it was renamed ‘Mur’ for mangenese uptake regulator [6,7]. Instead, many a-proteobacteria contain another transcriptional repressor called Irr (iron responsive reg- ulator) which, although a member of the Fur super- family, has important features that distinguish it from Fur sensu stricto (see below). Irr functions to repress a wide range of genes under low iron availability by binding to cis-acting regulatory sequences known as iron control element (ICE) boxes that are 5¢ of the target genes. It was first discovered in Bradyrhizobi- um japonicum [8–12] and was also studied in Rhizo- bium leguminosarum, where it represses a wide range of genes in cells grown under iron-depleted conditions [13,14], and in Brucella abortus, where it regulates siderophore biosynthesis [15]. In addition to Irr, a-pro- teobacteria that are closely related to Rhizobium, Agro- bacterium, Brucella and Bartonella contain another wide-ranging iron-responsive regulator called RirA [16–19]. RirA belongs to the Rrf2 family of regulators, which includes IscR and NsrR [20,21] and, similar to them, is a predicted FeS cluster-binding protein. RirA represses many genes under iron-replete conditions, recognizing the cis-acting iron regulatory sequences (RirA-boxes) that precede genes similar to those that are commonly regulated by Fur in other organisms [5,16–19]. Thus, RirA and Irr are ‘opposing’ regula- tors, which repress different portfolios of target genes in cells grown in sufficient (RirA) or deficient (Irr) lev- els of iron. Because these two regulators respond to the availability of iron in the form of iron-sulfur clus- ters and heme, respectively, and exhibit regulatory ‘cross-talk’ in response to iron availability [14], they may represent a combined regulatory system that senses the physiologically relevant status of iron and not just the concentration of the metal per se, as is the case in those organisms that use Fur or DtxR [13]. Few Irr proteins have been studied in detail so far. The first, from B. japonicum (Irr Bj ), exhibits a highly unusual regulatory mechanism. Under iron-replete conditions, Irr Bj interacts with heme at two known sites: an N-terminal heme regulatory motif (HRM) and an internal, histidine-rich (HxH) motif [12], with the heme being normally delivered to Irr Bj by ferroch- elatase [22]. The heme-Irr Bj complex is extremely unstable and is rapidly degraded. The mechanism by which this remarkable response occurs is not known but may involve heme- and oxygen-mediated oxidative damage that acts as signal(s) for protease-mediated degradation [23]. The end result is that, under iron- replete conditions, Irr Bj is unavailable to act as a repressor. Another member of the rhizobia, R. leguminosarum, which forms nodules on peas, clovers and beans, has an Irr (Irr Rl ) that is 57% identical to Irr Bj but lacks the N-terminal heme regulatory motif. We recently reported that Irr Rl functions by a very different mecha- nism that does not involve degradation in response to elevated iron. Instead of being degraded, the interac- tion between Irr Rl and heme causes an allosteric change in the protein, which prevents it from binding to its cognate ICE box DNA sequences [24]. In vitro studies showed that specific binding to DNA was abol- ished by the direct addition of heme, and spectroscopic studies of heme binding to wild-type Irr Rl and mutant forms of the protein revealed two low-spin ferric heme-binding sites. Substitution of the HxH motif abolished one of these sites, with a concomitant loss of DNA binding in vitro and regulatory function in vivo, demonstrating a key role of this motif [24]. The prop- erties and location of the second, lower-affinity heme- binding site of Irr Rl have not been fully investigated, although electron paramagnetic resonance (EPR) and magnetic CD spectroscopic studies showed that the heme bound at the second heme site is coordinated by two His residues [24]. In the present study, we used spectroscopic and bioanalytical methods to gain Heme binding to Irr promotes oligomerization G. F. White et al. 2012 FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS further insight into heme binding by R. leguminosarum Irr, with a focus on the second heme-binding site. These studies highlight important new features of Irr that have relevance to Irr proteins from a wide range of a-proteobacteria. Results Identification of the second heme-binding site of Irr Rl : importance of His46 and His66 It was previously shown that the second heme-binding site of Irr Rl is associated with low-spin S = ½ heme with g-values of 2.95, 2.26 and 1.55, and a near-infra- red magnetic CD band centred at approximately 1580 nm [24], demonstrating that the second heme iron has bis-His ligation [25]. However, these previous stud- ies did not establish which His residues are involved. In total, Irr Rl has seven His residues (Fig. 1A), three of which are at the HxH motif (His93, His94 and His95). One or more of the remaining His residues (His39, His46, His66 and His128) must therefore supply the ligands for the second heme site. A set of variants, in which each of these His residues was substituted with alanine, had been previously generated and their absolute heme spectra measured [24]. Although the spectra were similar in form to the wild- type Irr Rl spectrum, indicating no change in the ratio of high- to low-spin bound heme, the amounts of heme bound differed according to which histidine had been substituted. Thus, variants H39A and H128A were essentially identical to the wild-type Irr Rl protein, whereas H46A and H66A exhibited spectra with signif- icantly lower heme intensity [24]. Consistent with this, hemochromogen analyses revealed that, although H39A and H128A Irr Rl proteins bound only margin- ally less heme than wild-type ( 1.4 compared to  1.5 heme per protein), H66A ( 1.1 heme per pro- tein) and H46A ( 0.9 heme per protein) exhibited sig- nificantly lower heme binding (not shown). EPR spectra of each of the single His variants were recorded. Previous studies showed that the heme that binds at the HxH motif is EPR silent, very likely result- ing from the magnetic coupling of HxH hemes within a BA DC Fig. 1. Spectroscopic studies of Irr Rl His variants. (A) Amino acid residue sequence of Irr Rl , with His residues highlighted. (B) EPR spectra of wild-type (black), H39A (green), H46A (blue), H66A (purple) and H128A (orange) Irr variants. (C) UV-visible absorbance and (D) EPR spectra of H93 ⁄ 94 ⁄ 95A (red), His39 ⁄ 93 ⁄ 94 ⁄ 95Ala (olive green), His39 ⁄ 46 ⁄ 93 ⁄ 94 ⁄ 95Ala (dark cyan), His39 ⁄ 46 ⁄ 66 ⁄ 93 ⁄ 94 ⁄ 95Ala (magenta) and His- free (grey) Irr variants. Note that UV-visible and EPR spectra of wild-type and H93 ⁄ 94 ⁄ 95A Irr were reported previously [24] and are included here for reference. Excess heme was added to each protein and non- or weakly-bound protein was removed by gel filtration and the protein concentrated as necessary. Proteins (10 l M for absorbance, 100 lM for EPR) were in 50 mM Tris-HCl, 50 mM KCl (pH 8). EPR measurement conditions were: temperature, 10 K; microwave power, 2 mW; modulation amplitude, 10 G. G. F. White et al. Heme binding to Irr promotes oligomerization FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS 2013 proposed Irr dimer [24]. Therefore, the low-spin heme signals observed in the EPR spectrum are the result of a heme bound at the second heme site. We noted that the low-spin heme signal intensity was decreased in both the H46A and H66A variants, although it was unaf- fected by substituting His39 or His128 (Fig. 1B), sug- gesting that His46 and His66 may be involved in binding heme at the lower-affinity site. This raised the question of why EPR-active low-spin heme binding was not completely abolished in one or more of these vari- ants. One explanation for this is that a minority of the heme bound at the HxH site may not be magnetically coupled, most likely as a result of incomplete occupa- tion, which would result in a small component of the HxH-bound heme being EPR-active. Alternatively, loss of the second heme site ligands could interfere with cou- pling of heme at the HxH site. In either case, inactiva- tion of both heme-binding sites would be required to abolish all low-spin heme binding. To test this model, a further set of site-directed vari- ants was generated. Beginning with the H93 ⁄ 94 ⁄ 95A variant (in which the three His residues at the HxH motif are substituted for Ala residues and previously referred to as the HHH variant) [24], each of the remaining His residues was substituted stepwise, sequentially generating H39 ⁄ 93 ⁄ 94 ⁄ 95A, H39 ⁄ 46 ⁄ 93 ⁄ 94 ⁄ 95A and H39⁄ 46 ⁄ 66 ⁄ 93 ⁄ 94⁄ 95A, as well as an entirely His-free Irr Rl protein, H39 ⁄ 46 ⁄ 66 ⁄ 93 ⁄ 94 ⁄ 95 ⁄ 128A (His-free Irr Rl ). The far-UV CD spectrum of the fully His-free variant indicated that the protein was folded with a secondary structure content similar to the wild-type protein (Fig. S1). UV-visible absorbance (Fig. 1C) and EPR analysis (Fig. 1D) of this His-free variant after the addition of heme revealed only weak, nonspecific (adventitious) binding (Fig. S2). Having established the baselines for the fully His-free form of Irr Rl , we used UV-visible absorbance to examine heme binding to the Irr Rl variants that retained at least one histidine residue (Fig. 1C). The data obtained showed that, as additional His residues were substituted, the form of the spectrum changed, with that of H39 ⁄ 93 ⁄ 94 ⁄ 95A being similar to the H93 ⁄ 94 ⁄ 95A variant, whereas that of H39 ⁄ 46 ⁄ 66 ⁄ 93⁄ 94 ⁄ 95A more closely resembled the His-free variant. This reflects a decrease in the proportion of heme binding in the low-spin con- figuration and is consistent with a progression towards only low-affinity adventitious, high-spin heme binding in the absence of His residues (Fig. S2). EPR spectra of the multi-His variants were recorded (Fig. 1D). These showed that the ability to bind low-spin heme was significantly diminished in the H39 ⁄ 93 ⁄ 94 ⁄ 95A variant, and was lost entirely in H39 ⁄ 46 ⁄ 93 ⁄ 94 ⁄ 95A Irr Rl . Irr Rl stabilizes heme in the ferric form Previous studies of heme binding to Irr from B. japoni- cum indicated that the protein has both ferric and fer- rous heme-binding sites [12]. To investigate whether Irr Rl has a specific ferrous heme-binding site, Irr Rl was titrated with heme at pH 7 using reduced hemin under anerobic conditions in the presence of a two-fold excess of sodium dithionite. As shown by UV-visible absorbance spectra, heme was bound in a reduced state, almost all of which was in the low-spin form, with the Soret band at 426 nm and resolved a ⁄ b bands at 528 and 559 nm [24] (Fig. 2A). Measurements of A 426 (converted to fractional saturation) fitted well to a single site model, giving a K d of 1 ± 0.2 · 10 )6 m (Fig. 2A, inset). This indicated that ferrous heme has a significantly lower affinity than ferric heme (K d =1· 10 )7 m) [24] (Fig. S3), and that ferrous heme apparently binds at only one of the two heme- binding sites of Irr Rl . Upon removing dithionite under anerobic conditions, the UV-visible absorbance spec- trum revealed that heme was bound only in the oxi- dized state (not shown), consistent with a higher affinity binding of ferric heme. Heme binding to proteins is commonly pH-depen- dent [26–28] and thus heme binding in both the oxi- dized and reduced states was investigated at higher pH. In the oxidized state, although the affinity was found by absorbance and fluorescence titrations to decrease somewhat with increasing pH (Doc. S1 and Fig. S3A, B), the form of heme binding (as judged from difference and absolute UV-visible spectra) was unaltered (Doc. S1 and Fig. S3C). By contrast, at pH 8, the reduced heme UV-visible difference spectrum was quite different from that at pH 7, indicating that only ferric heme was bound to the protein (Fig. 2B). Even at a five-fold excess of dithionite, a mixture of reduced and oxidized heme was observed, which again was all converted to oxidized heme upon the anerobic removal of excess dithionite (data not shown). Although there is no indication that heme undergoes redox cycling in Irr Rl , we attempted to determine the reduction potential of Irr Rl -bound heme. Spectropoten- tiometric titration experiments at pH 7 using dithionite in the presence of mediators were unsuccessful because a significant reduction of heme was not observed in the accessible potential range (data not shown), consis- tent with Irr Rl -bound heme having a very low reduc- tion potential (i.e. similar to, or lower than, that of the HSO 3 ) ⁄ S 2 O 4 2) couple of < )500 mV at pH 7) [29]. Thus, Irr Rl has a considerable preference for heme in the ferric state, and strongly promotes the oxidation of heme when it encounters this ligand in the ferrous Heme binding to Irr promotes oligomerization G. F. White et al. 2014 FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS form. Therefore, it is clear that Irr Rl does not contain a ferrous heme-binding site. Heme binding to Irr Rl promotes oligomerization The pathogen B. abortus is a member of the Rhizobi- ales that is more closely related to Rhizobium than it is to Bradyrhizobium. Its Irr protein (Irr Ba ) also more clo- sely resembles Irr Rl (67% identical) than Irr Bj (56% identical) and it lacks the N-terminal HRM. Gel filtra- tion studies on purified Irr (Irr Ba ) from this species had shown that it is likely dimeric [30], as are other members of the Fur superfamily [31,32]. To analyse the association state of Irr Rl , analytical gel filtration experiments were performed. For the ‘as isolated’, heme-free protein, two distinct peaks were detected in the chromatograph (Fig. 3A). Thus, the heme-free pro- tein exists as an equilibrium mixture of two principal association states, which must be in slow exchange, such that they can be separated by gel filtration. Cali- bration of the column suggested that the lower molec- ular weight species corresponds to a dimeric form, consistent with our previous proposal that heme bound at the HxH motif of Irr Rl is EPR-silent as a result of magnetic coupling between two closely located HxH- bound hemes. The higher molecular weight species cor- responded to a much larger, oligomeric form, although this could not be precisely defined by gel filtration alone. Interestingly, addition of heme to Irr Rl resulted in significant changes in the elution profile: only one major band was observed, corresponding to the higher molecular weight species (Fig. 3A). Analysis of elution data at different wavelengths confirmed that the observed profile changes were the result of a change in the distribution between higher and lower molecular weight species and not the preferential binding of heme to the larger species (Fig. S4). Heme binding, however, did not cause major changes in the secondary structure because far-UV CD spectra of Irr Rl before and after the addition of heme were very similar (Fig. 3B). To determine the mass of the oligomeric species more precisely, analytical ultracentrifugation experi- ments were run for heme-Irr Rl at five different concen- trations, in the range 5–19 lm, at 15 000 and at 17 000 r.p.m. Figure 3C shows the data obtained for one representative concentration of heme-Irr Rl (10 lm). Fitting of the data, at both speeds and for all concen- trations, to a single component model gave a mass of 96.6 ± 8 kDa for the heme-bound Irr Rl sample (resid- uals for the fits are shown in the inset to Fig. 3C). The data thus indicate that the higher molecular weight species of Irr Rl corresponds to a hexamer. To examine the role (if any) of the HxH motif in the heme-dependent oligomerization, the association state of the H93 ⁄ 94⁄ 95A mutant Irr Rl was also investi- gated. The gel filtration profile (Fig. 3D) was very sim- ilar to that of the wild-type protein, and the addition of heme to the mutant polypeptide caused a similar shift in equilibrium towards the larger (hexameric) spe- cies. Therefore, the process of oligomerization is not directly connected to heme binding at the HxH motif and must be associated with heme binding at the lower-affinity site. To test this proposal, Irr Rl variants containing single substitutions of His residues consid- ered to be involved in heme binding were examined by analytical gel filtration. H46A and H66A Irr Rl proteins AB Fig. 2. Binding of ferrous heme by Irr Rl . (A) UV-visible difference absorbance spectra recorded upon titration of ‘as isolated‘ (heme-free) Irr (17 l M)in50mM Tris-HCl, 50 mM KCl (pH 7) with ferrous heme. The trend of absorption changes are indicated by arrows. The inset shows a plot of fractional saturation (from DA 426 ) as a function of reduced heme concentration. A fit of the data to a single site model is drawn. Pathlength, 1 cm; temperature, 20 °C. (B) UV-visible difference absorbance spectra as recorded in (A), except that the pH of the Irr (18 l M) solution was 8. Note that the form of the difference titration was different from that observed for the oxidized heme titration (Fig. S3A), although this is because hemin remained in the ferrous state in the reference cuvette, thereby imparting a different form on the difference spectrum. G. F. White et al. Heme binding to Irr promotes oligomerization FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS 2015 exhibited somewhat different behavior to the wild-type and H93 ⁄ 94 ⁄ 95A proteins; oligomerization was still observed upon heme binding, although to a signifi- cantly lesser extent, as judged by the more prominent peak due to the dimeric protein remaining after the addition of heme (Fig. 4A). A simple analysis of absorbance changes indicated that oligomerization of H46A and H66A Irr Rl in the presence of heme was approximately 60% of that observed for the wild-type protein (Fig. 4B, C). A decreased level of oligomeriza- tion was also observed in the His-free variant, although this was both before and after the addition of heme. By contrast, H39A, H93A, H94A and H95A all behaved similarly to the wild-type and H93 ⁄ 94 ⁄ 95A proteins (Fig. 4). Discussion The transcriptional regulator Irr represents something of a signature polypeptide for the a-proteobacteria, being found in no other bacterial lineages [5]. How- ever, it has only been studied directly in a few species, namely B. japonicum, R. leguminosarum and, to a lesser extent, B. abortus, all of which are in the same Order (the Rhizobiales). These studies have shown that Irr is a remarkable protein, sensing iron in the form of heme, which, on binding to Irr, exerts unusual effects on the protein that cause it to lose its repressive, DNA-binding ability. It is clear that the Irr proteins of different bacteria have much in common because they recognize the same conserved ICE box sequences and these cis-acting elements are found in the operators of some genes (e.g. mbfA in R. leguminosarum corre- sponds to blr7895 in B. japonicum strain 110) that are equivalent in different species [14]. However, it is also apparent that there are significant differences in the behavior of Irr in different species. Thus, in B. japoni- cum, the interaction with heme results in a rapid and dramatic destruction of the Irr Bj , but, as we recently found, this does not occur in Rhizobium. Rather, when Irr Rl interacts with heme, this abolishes its DNA-bind- ing ability, although this does not destroy the polypep- tide [24]. This difference in behavior is at least partly a result of the different ways in which the proteins interact with heme. Although the proteins have a functionally A CD B Fig. 3. Bioanalytical studies of the association state of Irr Rl . (A) Analytical gel filtration plots of A 240 as a function of elution volume for sam- ples of Irr Rl (17 lM)in50mM Tris-HCl, 100 mM KCl, 10% (v ⁄ v) glycerol (pH 8) in the absence (apo) and presence of heme (two per protein), as indicated. (B) Far-UV CD spectra of wild-type Irr Rl with (grey line) heme (two per protein). The spectrum of Irr without heme (black line) [24] is shown to aid comparison. Irr (10 l M) was in 50 mM potassium phosphate (pH 8). Pathlength, 1 mm; temperature, 20 °C. (C) Analytical equilibrium ultracentrifugation plots of A 280 as a function of the radius after equilibration at 15 000 and 17 000 r.p.m. at 25 °C of Irr (10 lM in 50 m M Tris-HCl, 100 mM KCl, pH 8) containing two heme per protein, as indicated. A fit to a single component model is drawn on each plot and the residuals for each are shown in the inset. (D) Analytical gel filtration plots as in (A), except that H93 ⁄ 94 ⁄ 95A Irr was analyzed in the absence and presence of heme. Heme binding to Irr promotes oligomerization G. F. White et al. 2016 FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS important HxH motif in common that binds heme, this analyte also binds elsewhere. In the present study, we have focussed on understanding the nature of the second heme-binding site and its importance for the properties of Irr Rl . The most significant changes in the Irr Rl -heme absorbance spectrum occurred on substitu- tion of His46 or His66 [24], and the EPR low-spin heme signal intensity was reduced in His46 and His66 variants. Substitution of His39 or His128 (i.e. the other His residues present in Irr Rl outside of the HxH motif) had no effect on the UV-visible or EPR spectra, clearly indicating that these residues are not directly involved in heme binding. Furthermore, low-spin heme binding to Irr Rl already lacking the HxH motif was totally abolished when His46 was substituted. Unex- pectedly, substituting His39 in the H93 ⁄ 94⁄ 95A variant background resulted in a significant decrease in low- spin heme binding. Figure S5 shows that, in the previ- ously generated Irr Rl model (based on the available structures of Fur proteins) [24], His39 lies very close to the HxH motif, and it is possible that the combination of these substitutions, neither of which alone signifi- cantly affects heme binding at the second site, causes a conformational change that affects the second heme site, resulting in a loss of low-spin binding and an increase in high-spin heme (Fig. 1C, D). Taken together, the UV-visible and EPR data indi- cate that His46 is a key ligand at the second, lower- affinity heme site and that His66 is also important. Although not involved directly in heme binding, His39 is likely to play an important, but as yet undefined, role in Irr Rl because it is absolutely conserved among Irr proteins and in the wider Fur families, represented by Fur itself, the Zur and Mur regulators, and PerR, which respond to zinc, manganese and peroxide stress, respectively [33,34]. In these proteins, it serves as a ligand at a divalent metal ion binding site. By contrast to His39, His128 is not conserved in the Fur superfam- ily, nor in the Irr family, and therefore is unlikely to be involved in heme binding in Irr Rl . We note that His46 and His66 are conserved in the Irr proteins of other members of the Rhizobiaceae family, including the closely related Sinorhizobium and Agrobacterium, as well as in strains of Mesorhizobium (in the family Phyllobacteriaceae). Interestingly, all of these Irr pro- teins lack the heme-binding HRM found near the A CB Fig. 4. Analytical gel filtration studies of Irr Rl His variants. (A) Analytical gel filtration plots of relative A 280 as a function of elution volume for samples of wild-type, H46A and H66A Irr (17 l M), as indicated, in 50 mM Tris-HCl, 100 mM KCl, 10% (v ⁄ v) glycerol (pH 8) with no heme (apo) and after the addition of excess heme per protein and removal of unbound heme by passage down a PD10 column (indicated by ‘+ heme’). (B) Histogram plot of the ratio of absorbance as a result of the higher (hexameric) and lower (dimeric) molecular weight forms of Irr Rl , giving a quantitative indication of the extent of oligomerization in the apo- (grey bars) and heme-bound (black bars) forms. Data were obtained from (A) and from equivalent experiments on additional Irr Rl proteins, as indicated. (C) Histogram plot of the ratio of ratios for apo- and heme-bound Irr Rl proteins [i.e. the data in (B)], giving a direct quantitative indication of the extent of heme-induced oligomerization. A value of 1 indicates no change in association state upon binding heme. G. F. White et al. Heme binding to Irr promotes oligomerization FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS 2017 N-termini in Irr proteins from Bradyrhizobium and other members of the Bradyrhizobiaceae family, in which His46 and His66 are not present. On the basis of the Irr Rl model, we predict that His46 and His66 are located in the DNA-binding domain on consecutive a-helices that are connected by a loop (Fig. S5). In the model, the two His residues are not sufficiently close to cooperate in binding a sin- gle heme, although a conformational rearrangement of the helices could potentially align them appropriately. Alternatively, the second, lower-affinity heme binding may not be at an intrasubunit site but, instead, could be at an intersubunit site involving His residues from juxtaposed subunits. Even though the Irr Bj and Irr Rl proteins both con- tain an HxH motif, the binding characteristics of the motif in the two proteins are different. Irr Bj binds fer- rous heme at its HxH motif [12], whereas, in the pres- ent study, we have shown that both heme sites of Irr Rl have a very significant preference for ferric heme and do not bind ferrous heme in the absence of an excess of reductant. It remains unclear why the Irr Rl and Irr Bj HxH motifs should exhibit different heme iron oxida- tion state preferences. The propensity of Irr Rl to oligomerize has also been demonstrated in the present study, and this was enhanced by heme binding at the lower-affinity heme site associated with His46 and His66. Because Irr Bj lacks an equivalent site, we anticipate that it might exhibit different behavior, although the association state prop- erties of the Bradyrhizobium Irr have not yet been inves- tigated. Irr Ba was found to be a dimer and no evidence of oligomerization was reported [30]. Irr is a member of the Fur superfamily and it has long been known that Fur itself can exist in oligomeric forms in solution, as well as when bound to DNA [35,36]. Furthermore, we noted that high molecular weight forms of Irr Rl occur in whole cell extracts of R. leguminosarum [24]. Currently, the functional roles of the second heme site and of oligomerization remain unclear because variants disrupted in heme binding at this site were not affected in their ability to bind DNA, nor were they significantly affected in their ability to function in vivo [24]. However, the conservation of the site ligands, together with their importance for the properties of the protein in vitro, in heme binding and in oligomeriza- tion, suggests that this site has functional importance. Clearly, further studies are required to understand bet- ter the role of the second heme site and the functional consequences of heme-induced oligomerization. For example, it is not known whether the dimeric or hexa- meric (or both) form of Irr Rl can bind ICE box DNA sequences. Given the remarkable variation in the properties of the very few Irr proteins that have been studied directly, it will be of interest to examine the somewhat more distantly related versions of Irr in other Orders of the a-proteobacteria, not least, members of the Rhodobacterales and the SAR 11 clade, which form the most abundant bacteria in the world’s oceans. Despite this, we still know almost nothing about their iron-responsive biology. Materials and methods Generation of sequential His variants of Irr Rl Mutagenesis on pBIO1632 (encoding wild-type Irr Rl )to individually substitute H93, H94 and H95 with alanine resi- dues was carried out using the primers listed in Table S1 and a QuikChange XL mutagenic PCR kit (Stratagene, La Jolla, CA, USA) in accordance with the manufacturer’s instructions, generating pBIO1839 (H93A), pBIO1840 (H94A) and pBIO1841 (H95A). Successive rounds of muta- genesis on pBIO1819 (encoding Irr Rl in which the H93, H94 and H95 residues are all substituted with the corre- sponding alanines; termed H93 ⁄ 94 ⁄ 95A Irr Rl ) and deriva- tives were carried as described above, resulting in the stepwise substitution of all of the His residues in Irr Rl with Ala, generating pBIO1820 (H39 ⁄ 93 ⁄ 94 ⁄ 95A), pBIO1821 (H39 ⁄ 46 ⁄ 93 ⁄ 94 ⁄ 95A), pBIO1822 (H39 ⁄ 46 ⁄ 66 ⁄ 93 ⁄ 94 ⁄ 95A) and, finally, pBIO1744, which encodes His-free (H39 ⁄ 46 ⁄ 66 ⁄ 93 ⁄ 94 ⁄ 95 ⁄ 128A) Irr Rl . Verified mutated plas- mids (Table S2) were used to transform Escherichia coli BL21(DE3) for protein over-expression. Purification of wild-type and variant forms of Irr Rl and in vitro heme additions Wild-type and variant Irr Rl proteins were purified in a heme-free form as previously described [24] and exchanged into 50 mm Tris-HCl, 50 mm KCl (pH 7 or 8, as req- uired). Protein concentrations were determined using an e 280 nm of 5800 m )1 Æcm )1 obtained from amino acid analy- sis (Alta Biosciences, Birmingham, UK). For spectroscopic and analytical studies, heme additions were made using a micropipette (Gilson Inc., Middleton, WI, USA) or a mi- crosyringe (Hamilton, Reno, NV, USA). For UV-visible difference absorption titration experiments, Irr was added to the sample cuvette and heme additions were made to the sample and reference cuvettes. Heme solutions ( 1mm) were freshly prepared as described previously [24]. Bound heme concentrations were determined using a modified version of the hemochromogen method [37] as described previously [24]. For ferrous heme titrations, hemin was reduced using a two-fold molar excess of sodium dithionite. Heme binding to Irr promotes oligomerization G. F. White et al. 2018 FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS Spectroscopic and bioanalytical methods UV-visible absorption spectra were recorded using a Hitachi U-4010 or U-2900 spectrophotometer (Hitachi Corp., Tokyo, Japan). EPR spectra were measured using an X-band spectrometer (Bruker ER200D; Bruker, Rheinstet- ten, Germany) with an EPS 3220 computer system (Bruker) fitted with an ESR9 liquid helium flow cryostat (Oxford Instruments, Abingdon, UK). Spin intensities of paramag- netic samples were estimated by double integration of EPR signals measured at 15 K using 1.25 mm Cu 2+ ,10mm EDTA as the standard. Binding isotherms obtained from spectroscopic titrations of Irr Rl with heme were analyzed using origin, version 7 (Microcal; OriginLab Corporation, Northampton, MA, USA) employing a single binding site model (where the free ligand concentration was unknown) and ⁄ or the software dynafit (Biokin, Watertown, MA, USA) for single-site and two-site binding models [38]. Sedi- mentation-equilibrium experiments were performed using a Beckman XL-I analytical ultracentrifuge in an AN50Ti rotor (Beckman Coulter, Brea, CA, USA) at 25 °C, in 12 mm charcoal-filled Epon double-sector cells with quartz windows. The sample volume was 110 lL and the reference sector of the cell contained identical buffer. Samples of Irr Rl containing heme at five different concentrations were spun at 15 000 or at 17 000 r.p.m. until equilibrium was reached, as judged by cessation of changes in scans collected 4 h apart. Data were collected at 280 nm and analyzed using ul- traspin, version 2.5 (http://ultraspin.mrc-cpe.cam.ac.uk/). The density of the buffer was taken as 1.005 gÆmL )1 and the partial specific volume of Irr Rl was calculated to be 0.7421 mLÆg )1 using the software sednterp [39]. Analytical gel filtration of samples of Irr Rl utilized a Superdex 75 col- umn (GE Healthcare), equilibrated in 50 mm Tris-HCl, 50 mm KCl, 10% glycerol (v ⁄ v) (pH 8.0) and operated at a flow rate of 0.8 mLÆmin )1 . The column was calibrated using cytochrome c (12.4 kDa), carbonic anhydrase (29 kDa), bovine serum albumin (66 kDa) and alcohol dehydrogenase (150 kDa). Acknowledgements This work was supported by the UK BBSRC through the award of grant BB ⁄ E003400 ⁄ 1, to A.W.B.J. and N.E.L.B., and the Wellcome Trust through an award from the Joint Infra-structure Fund for equipment. We thank Dr Tom Clarke for assistance with the AUC experiments. 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White et al. 2020 FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS [...]... analysis of the association state of heme- bound IrrRl Fig S5 Model of IrrRl Heme binding to Irr promotes oligomerization Doc S1 pH dependence of ferric heme binding to IrrRl Table S1 Oligonucleotide primers used in the present study Table S2 Plasmids used in the present study This supplementary material can be found in the online version of this article Please note: As a service to our authors and readers,... Rowe AJ & Horton J eds), pp 90–125 Royal Society of Chemistry, Cambridge Supporting information The following supplementary material is available: Fig S1 Folding properties of the His-free variant of IrrRl Fig S2 UV-visible absorbance studies of heme binding to IrrRl His-free variant Fig S3 UV-visible absorbance and fluorescence studies of heme binding to IrrRl Fig S4 Gel filtration analysis of the association... this journal provides supporting information supplied by the authors Such materials are peer-reviewed and may be re-organized for online delivery, but are not copy-edited or typeset Technical support issues arising from supporting information (other than missing files) should be addressed to the authors FEBS Journal 278 (2011) 2011–2021 ª 2011 The Authors Journal compilation ª 2011 FEBS 2021 . Heme binding to the second, lower-affinity site of the global iron regulator Irr from Rhizobium leguminosarum promotes oligomerization Gaye F. White 1,2 , Chloe Singleton 1 , Jonathan D. Todd 2 ,. insights into the mecha- nisms and consequences of heme binding to Irr. In addition to the HxH motif, Irr binds heme at a second, lower-affinity site. Spectroscopic studies of wild-type Irr and His. of heme binding to Irr from B. japoni- cum indicated that the protein has both ferric and fer- rous heme- binding sites [12]. To investigate whether Irr Rl has a specific ferrous heme- binding site,