A Transition Metal-Binding, Trimeric Î²Î³-Crystallin from Methane

Article pubs.acs.org/biochemistry

A Transition Metal-Binding, Trimeric βγ-Crystallin from MethaneProducing Thermophilic Archaea, Methanosaeta thermophila Shanti Swaroop Srivastava, Aditya Anand Jamkhindikar, Rajeev Raman, Maroor K. Jobby, Swathi Chadalawada, Rajan Sankaranarayanan,* and Yogendra Sharma* CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad 500 007, India ABSTRACT: βγ-Crystallins are important constituents of the vertebrate eye lens, whereas in microbes, they are prevalent as Ca2+-binding proteins. In archaea, βγ-crystallins are conspicuously confined to two methanogens, viz., Methanosaeta and Methanosarcina. One of these, i.e., M-crystallin from Methanosarcina acetivorans, has been shown to be a typical Ca2+-binding βγcrystallin. Here, with the aid of a high-resolution crystal structure and isothermal titration calorimetry, we report that “Methallin”, a βγ-crystallin from Methanosaeta thermophila, is a trimeric, transition metal-binding protein. It binds Fe, Ni, Co, or Zn ion with nanomolar affinity, which is consistent even at 55 °C, the optimal temperature for the methanogen’s growth. At the center of the protein trimer, the metal ion is coordinated by six histidines, two from each protomer, leading to an octahedral geometry. Small-angle X-ray scattering analysis confirms that the trimer seen in the crystal lattice is a biological assembly; this assembly dissociates to monomers upon removal of the metal ion. The introduction of two histidines (S17H/ S19H) into a homologous βγ-crystallin, Clostrillin, allows it to bind nickel at the introduced site, though with micromolar affinity. However, because of the lack of a compatible interface, nickel binding could not induce trimerization, affirming that Methallin is a naturally occurring trimer for high-affinity transition metal binding. While βγ-crystallins are known to bind Ca2+ and form homodimers and oligomers, the transition metal-binding, trimeric Methallin is a new paradigm for βγ-crystallins. The distinct features of Methallin, such as nickel or iron binding, are also possible imprints of biogeochemical changes during the period of its origin. he βγ-crystallin domains are prevalent in a wide variety of proteins in combination with various domains and are found in many organisms from bacteria to mammals (for recent reviews, see refs 1−3). Proteins containing this domain that is comprised of two Greek key motifs are collectively categorized under the banner of the βγ-crystallin superfamily.4,5 Most studies of βγ-crystallins have been conducted in the context of eye lenses, focusing on their stability, genetics, and implications in cataractogenesis.3,6,7 Some scattered reports of nonlenticular roles are also available.3 Other studies of non-lens eukaryotic βγ-crystallins from yeast, invertebrates, and mammals along with bacterial systems have shed light on their diversity, molecular properties, and evolutionary connections, suggesting a common ancestral origin.2,8−14 Despite their wide distribution, their physiological roles are still poorly understood, except for their Ca2+ binding properties in microbes and structural roles in vertebrate eye lenses.1−3,6,15 It has also been suggested that the ancestral Ca2+ binding features of βγ-crystallins were lost during the course of evolution for their recruitment as lens proteins.15−18 Sequence analysis revealed that βγ-crystallins are represented only in three archaeal species belonging to the order Methanosarcinales, viz., Methanosaeta thermophila, Methanosarcina acetivorans, and Me. barkeri, portraying a highly selective recruitment2 [data from the whole genome sequence of >200 archaeal species available in the KEGG database Organisms:

T

© XXXX American Chemical Society

Complete Genomes (http://www.genome.jp/kegg/catalog/ org_list.html)] (Figure 1A). Interestingly, Methanosarcina and Methanosaeta are the only two genera that constitute acetateutilizing methanogenic archaea and are considered as major contributors (approximately two-thirds) to global biologically produced methane.19,20 Methanogenic archaea have played a pivotal role in shaping life on earth, and therefore, the study of methanoarchaea and the components of methanogenesis constitutes an essential part of chronicling the earth’s atmosphere and life.21−24 In addition, being a source of biological methane production, methanogenic archaea attract immense interest for their prospects in renewable energy.25 M-Crystallin from Me. acetivorans is the only archaeal βγCrystallin that has been studied so far.26 It has been reported as a single-domain Ca2+-binding βγ-crystallin, harboring two binding sites like βγ-crystallin does, such as Ci-βγ-crystallin (urochordate), Spherulin 3a (slime mold), and bacterial βγcrystallins, such as Protein S, Clostrillin, and Flavollin, but it is similar to vertebrate lens βγ-crystallins in the arrangement of its motifs.1,9,12,26,27 The other Methanosarcina species whose genes encode M-crystallin are three strains of Me. barkeri MS, 227, Received: September 27, 2016 Revised: December 21, 2016 Published: December 28, 2016 A

DOI: 10.1021/acs.biochem.6b00985 Biochemistry XXXX, XXX, XXX−XXX

Article

Biochemistry

Figure 1. Recruitment of βγ-crystallins in specific archaea. (A) Schematic representation of methanoarcheal βγ-crystallins. According to current sequence database information, only three species of archaea have βγ-crystallins. (B) Sequence alignment highlighting similarities and differences in sequence features. Along with the signal sequence, Methallin shows variations in Y/FXXXXY/FXG and Ca2+-binding N/D-N/D-X1-X2-S/T-S motifs.

induced by 1 mM isopropyl β-D-1-thiogalactopyranoside for 3− 4 h postinduction at 37 °C. E. coli cells containing Methallin (83 amino acids) were lysed by ultrasonication in 10 mM imidazole hydrochloride (pH 7.1) containing 10 mM NaCl and 1 mM EDTA (lysis buffer). Methallin was expressed as a soluble protein in E. coli and was purified on a Mono-Q column (GE Healthcare Life Sciences) equilibrated with lysis buffer by a 10 to 300 mM linear gradient of NaCl. The major fraction of the Methallin V38R/L40R mutant passed through the column unbound as flow-through even at pH 8.5. The flow-through was adjusted to pH 7.0 and was further subjected to an SPSepharose column (GE Healthcare Life Sciences). Ion exchange chromatographic purifications were followed by gel filtration on a Superdex 75 prep grade column (GE Healthcare Life Sciences) equilibrated in 10 mM imidazole hydrochloride (pH 7.1) containing 50 mM KCl. The eluted fractions containing homogeneous protein were pooled, concentrated, and buffer-exchanged to the desired buffer. Purification of the Clostrillin S17H/S19H mutant was followed using methods described previously for the wild-type protein.29 Sequence alignments were performed using MultAlin30 and EsPript.31 Crystallization, Data Processing, and Refinement. The initial crystallization hits for Methallin were obtained from an Index screen of Hampton Research using the sitting drop vapor diffusion method. In addition, crystals that diffracted well were obtained by the hanging drop vapor diffusion method with a drop size of 4 μL [2 μL of protein, 8−12 mg/mL, and 2 μL of a reservoir solution, i.e., 17.5% PEG 8K, 0.1 M Tris-HCl (pH 9.0), and 0.01 M NiCl2]. The Clostrillin S17H/S19H mutant was crystallized with 5 mM NiCl2 under conditions similar to those described previously for the wild-type protein.12 X-ray diffraction data were collected on a home source (for Methallin, a Rigaku RU-H3R rotating anode generator equipped with an Osmic mirror system, operated at 50 kV and 100 mA, using a mar345dtb image plate detector, and for Clostrillin S17H/ S19H, an FR-E+ SuperBright microfocus rotating anode generator operated at 45 kV and 55 mA using an R-AXIS IV image plate detector). The oscillation widths for Methallin and

and CM1. M-Crystallins from these Me. barkeri strains share 86% sequence identity with that of Me. acetivorans and have canonical N/D-N/D-X-X-S/T-S Ca2+-binding motifs (Figure 1B). However, the physiological roles of M-crystallin in Methnaosarcina remain unknown. The methanogen M. thermophila also has a βγ-crystallin annotated as “hypothetical protein Mthe_0038” (accession no. NC_008553). Unlike Mcrystallin, the uncharacterized βγ-crystallin from M. thermophila that we name here “Methallin” (Methanosaeta + crystallin) does not have the canonical Ca2+-binding motifs and lacks some of the conserved residues in the β-hairpin motif. It also differs from M-crystallin in having a long N-terminal signal sequence of 50 residues as predicted by SignalP 2.0 HMM28 (Figure 1A,B). The exclusive features of two βγ-crystallins from acetoclastic methanogenic archaea prompted us to examine the possible significance of these variations, which led to an unanticipated finding of a trimeric, transition metal-binding βγcrystallin. The results obtained provide a new outlook for the roles of βγ-crystallins, in addition to opening a new avenue for the discovery of novel transition metal-based pathways in M. thermophila.

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EXPERIMENTAL PROCEDURES Cloning, Site-Directed Mutagenesis, Overexpression, and Purification. Genomic DNA of M. thermophila (strain NBRC 101360T) was a kind gift from K. Mori [National Biological Resource Centre (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan] and Y. Kamagata [National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan]. Gene-specific primers were used to amplify the crystallin domain (amino acids Ala57−Ser138) of the protein Methallin (Figure 1A). The resulting polymerase chain reaction product was ligated into NdeI and BamHI sites in a pET21a vector. The vector containing the methallin gene was transformed into Escherichia coli BL21(DE3) Rosetta-Origami (Novagen) for overexpression in LB broth containing 0.4% D-glucose until the A600 reached 0.6−1.0. Heterologous protein overexpression was B


Article

Biochemistry

Figure 2. Crystal structure of βγ-crystallin “Methallin” from the methanoarchaea M. thermophila. (A) Cartoon representation of crystal structure of Methallin. Three molecules of Methallin are present in the asymmetric unit forming a distinctive trimer. At the center of the trimer on the trimer axis, a transition metal is present. (B) A protomer of Methallin is comprised of two Greek key motifs (colored in purple and red shades) with the βstrands forming a typical βγ-crystallin domain. Two histidine residues (His14 and His16), which coordinate the metal ion, are located on the second β-strand. (C) Electrostatic representation of the trimer showing the electronegative (red) and electropositive (blue) surface present on opposite sides of the metal-binding site. (D) Electron density map showing histidine residues coordinating a transition metal ion. The 2Fo − Fc map (light blue) is contoured at 1.5σ, whereas the Fo − Fc map (red) is contoured at 5σ. (E) Stereoimage depicting the two histidines coming from each protomer of the trimeric protein coordinating the metal ion in an octahedral geometry.

Small-Angle X-ray Scattering (SAXS) Studies. Scattering was measured using a 6 mg/mL Methallin solution for 1 h at a wavelength of 1.5418 Å. The scattering intensity was recorded on a 487 × 195 pixel Pilatus 100 K detector, situated 300 mm from the sample, associated with the Hecus system being operated at 50 kV and 1 mA. After Azimuthal averaging of raw data with the help of the program FIT2D,41 analysis of scattering data and ab initio model generation were performed using the ATSAS suite of programs.42 PRIMUS43 was used for the calculation of the radius of gyration (Rg). The GNOM program was used to calculate Dmax and the P(r) distance distribution function.44 Ab initio models were prepared using the DAMMIN program.45 CRYSOL was used to evaluate the X-ray solution scattering curves from atomic models.46 Size Exclusion Chromatography. The oligomeric status of Methallin was evaluated on a Superdex200 10/300GL column (GE Healthcare). For the Methallin V38R/L40R mutant, a Superdex75 10/300GL column (GE Healthcare) was used. Throughout the experiment, only Chelex-purified buffers [e.g., 25 mM HEPES containing 50 mM KCl (pH 7.5)] were used. Molecular mass marker kits [containing Blue Dextran, albumin (67 kDa), ovalbumin (43 kDa), carbonic anhydrase (29 kDa), chymotrypsinogen A (25 kDa), and ribonuclease A

Clostrillin S17H/S19H were 1° and 0.5°, respectively. Data were processed using HKL2000,32 and for reflection file conversion, the CCP4 program suite was used.33 The unit cell parameters for Methallin that crystallized in space group C2 are as follows: a = 94.73 Å, b = 52.82 Å, c = 51.71 Å, α = 90.0°, β = 100.48°, and γ = 90.0°. The unit cell parameters for Clostrillin S17H/S19H that crystallized in space group I422 are as follows: a = b = 77.68 Å, c = 74.62 Å, and α = β = γ = 90.0°. The structure was determined by molecular replacement using PHASER in the PHENIX suite.34 A search model for Methallin was created by SWISS-MODEL using Protein Data Bank (PDB) entry 2BV2 (Ci-βγ-crystallin) as a template, while the previously reported structure of Clostrillin (PDB entry 3I9H) was used as a search model to determine the structure of the Clostrillin S17H/S19H mutant.9,12,35 The initial model was built using ArpWarp.36 Manual model building was performed in COOT.37 Iterative cycles of refinement were performed using the Phenix.refine program.38 The structures were validated using MolProbity.39 Figures were rendered using PyMol (The PyMOL Molecular Graphics System, version 1.2r3pre, Schrödinger, LLC). SSM, built into COOT, was used for structural superposition. Structure-based sequence alignment was performed with the help of Dali Server.40 C


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Biochemistry

Table 1. Crystallographic Data and Refinement Statisticsa

(13.7 kDa)] from GE Healthcare were used for column calibration. Atomic Absorption Spectroscopy (AAS). For the detection of bound metal in the purified protein, an atomic absorption spectrophotometer (PerkinElmer AAnalyst) was used. Before measurement, purified protein was thoroughly buffer-exchanged with Chelex-purified buffer [10 mM HEPES and 10 mM KCl (pH 7.5)]. The wavelengths used for Fe and Ni were 248.3 and 232 nm, respectively. Standard solutions were made by dissolving the FeSO4 and NiCl2 (from Sigma) in Chelex-purified Milli-Q water. For the calibration curve, 1, 2, 3, 4, and 5 ppm standard solutions were used. The calibration curve correlation coefficients for Fe and Ni standards were 0.999 and 0.998, respectively, and 1 mg/mL (∼100 μM) Methallin was used. Isothermal Titration Calorimetry (ITC). Ion binding was assessed on an iTC200 (GE, Microcal) at 30 and 55 °C. Methallin (200 μM) was titrated with 600 μM NiCl2, CoCl2, or ZnCl2 with an injection volume of 1 μL. The reference was obtained by titrating the buffer [50 mM HEPES (pH 7.5) and 100 mM KCl] under identical conditions. MOPS buffer (25 mM, pH 7.0) containing 50 mM KCl was used for Fe2+ titration, and conditions were set to mimic anaerobic conditions. To maintain the anaerobic condition, the protein and ligand (FeSO4) were thoroughly degassed. Sodium dithionate (10 mM) was added to the protein and FeSO4 solutions in an airtight chamber. Protein (550 μM) was quickly transferred to the iTC200 sample cell and Fe2+ (1 mM) in an injection syringe of the iTC200 sample cell. For ion binding studies with the Clostrillin S17H/S19H mutant, 125 μM protein was titrated with 2 mM NiCl2 and 4 mM CaCl2. Data analysis and curve fitting were performed using Origin software supplied by the vendor of iTC200.

X-ray source space group cell dimensions a (Å) b (Å) c (Å) α (deg) β (deg) γ (deg) resolution range (Å) total no. of observations no. of unique reflections completeness (%) Rmerge (%) ⟨I/(σ)I⟩ redundancy CC1/2 resolution (Å) no. of reflections Rwork (%) Rfree (%) no. of protein subunits per asymmetric unit no. of atoms protein ligand water RMSD bond lengths (Å) bond angles (deg) mean B value (Å2) protein metal ion water Ramachandran favored (%) Ramachandran outliers (%) Clash score PDB entry

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RESULTS Crystal Structure of the Single-Domain βγ-Crystallin “Methallin” from M. thermohila. The crystal structure of Methallin was determined by molecular replacement using Ciβγ-crystallin from Ciona intestinalis (PDB entry 2BV2) as the search model and refined to 1.86 Å resolution as shown in Figure 2 and Table 1. Like other βγ-crystallins, Methallin is comprised of two Greek key motifs, which swap their third βstrand to form a pseudosymmetric domain (Figure 2B).47,48 Sequence analysis of Methallin revealed that the signature sequence Y/FXXXXY/FXG for the βγ-crystallin type of Greek key motif, which spans the β-hairpin region, is variable in both Greek key motifs. In the first Greek key at the place of the second conserved aromatic residue, Gln is present (FADANQRG), while in the second Greek key, Ser occupies the place of the conserved Gly (YREPNFQS). Despite the occurrence of variations in signature residues, the β-hairpin pattern of Methallin is maintained (Figure 2B). Root-mean-square deviation (RMSD) values obtained from the structural superposition of Methallin on other βγ-crystallin domains range from 1.5 to 2.4 Å over 71−80 Cα atoms, indicating more structural similarity with eukaryotic βγ-crystallins than with bacterial βγ-crystallins as a consequence of poor sequence identity of approximately 11−18% with bacterial βγ-crystallins. Also, the conserved Trp residue and Tyr corner in the second Greek key motif reflect the AB type of motif arrangement, which is similar to that of vertebrate βγ-crystallins. The most striking feature is an unprecedented trimeric arrangement in the crystal lattice with a total buried surface area of 2305 Å2 (16.7%

a

Methallin

Clostrillin S17H/S19H

Cu Kα rotating anode C2

Cu Kα rotating anode I422

94.73 52.82 51.71 90.0 100.48 90.0 25.0−1.86 (1.93−1.86)

77.68 77.68 74.62 90.0 90.0 90.0 25.0−2.01 (2.08−2.01)

89144

63993

20985 (1930)

7877 (755)

98.8 (91.2) 4.5 (30.6) 29.5 (3.1) 4.2 (3.7) 0.999 (0.843) Refinement 24.25−1.86 20983 18.24 (20.97) 21.98 (27.63) 3

99.9 (98.8) 12.5 (44.9) 16.7 (3.4) 8.1 (6.8) 0.996 (0.752) 24.56−2.01 7874 19.95 (20.30) 23.63 (25.57) 1

2051 1914 1 136

736 693 1 42

0.007

0.007

0.961

0.929

29.1 21.9 38.1 92.9

28.1 41.8 33.7 98.8

0.0

0.0

0.8 5HT7

0.75 5HT8

Data in parentheses are for the highest-resolution shell.

per monomer) (Figure 2A,C). We identified electron density for a metal ion at the center of the protein on the axis of the trimer (Figure 2D). Coordination chemistry, geometry, and electron density suggested it was a transition metal. The metal ion is coordinated by six histidine residues (His14 and His16 from each protomer) (Figure 2D). These two histidine residues are a part of the second β-strand of the first Greek key motif with a GXHXH sequence, where Gly represents a signature residue (Figure 2B,D). Such a coordination, wherein six histidines from three subunits come together to form an ionbinding pocket with octahedral geometry (Figure 2E), is distinct.49−51 However, different modes of transition metal D


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Biochemistry

Figure 3. Methallin exists as a trimer in solution, and trimer formation is the result of metal binding. The protein forms a trimer in solution. (A) Guinier analysis of 6 mg/mL Methallin for the calculation of Rg. (B) Pair distribution curve of Methallin. (C) SAXS envelopes made using DAMFILT (smooth surface) and DAMAVER (mesh) along with the fitted crystal structure are shown in different views.45 Graphs were plotted in ORIGIN, and models were rendered using PyMOL. (D) Crysol output showing good agreement of SAXS data and the crystal structure of Methallin. Experimental scattering curve of 6 mg/mL Methallin (black squares) and theoretical scattering curves calculated from the crystal structure (red circles) and DAMFILT model (blue asterisks). (E) Size exclusion chromatogram of Methallin showing the protein eluting as a trimer (in the metalbound form obtained after purification, black line) or a monomer after the removal of the transition metal (in the apo form, red line). The addition of Ni2+ induces trimerization of monomers (blue line). Arrows represent molecular mass markers: (1) albumin (67 kDa), (2) ovalbumin (43 kDa), (3) chymotrypsinogen A (25 kDa), and (4) ribonuclease A (13.7 kDa).

became evident when the trimeric protein was found to change to the monomeric state if the ion was removed (chelated with the help of lowering pH and EDTA) as seen by size exclusion chromatography (Figure 3E). It is worth noting here that the purified protein elutes as a trimer, and thus, the protein is expected to be already in the metal ion-bound form (Figure 3E). Strongly bound metal necessitates the use of a pH jump or chemical denaturation along with EDTA treatment for the removal of the metal. Such a well-organized trimeric assembly of a single-domain βγ-crystallin has not been reported, though many single-domain βγ-crystallins are known to organize as homodimers.8,55 High-Affinity Binding of Transition Metal Ions Persists Even at 55 °C. On the basis of the clues obtained from electron density, coordination chemistry, and the strong requirement of a metal ion for the methanogen, the metal ion seen in the crystal structure was thought to be a 3d transition metal. Also, the crystallization condition has 10 mM NiCl2. However, in the crystal structure, the metal ion was modeled as iron as the purified protein elutes in the metalbound form in which the metal ion was detected as iron (using the atomic absorption spectrophotometer, PerkinElmer AAnalyst). The concentrations of Fe in the protein sample and corresponding buffer control were 1.632 and 0.087 mg/L, respectively (Figure 4A). The measured nickel concentrations in the protein sample and buffer control were 0.057 and 0.023 mg/L, respectively (Figure 4A). Thus, in 1 mg/mL (∼100 μM) Methallin, 1.632 mg/L Fe (∼30 μM) was detected, which

coordination via six histidines have also been seen in other completely different classes of proteins, such as Calprotectin,52 receptor-binding protein (RBP) from Staphylococcus aureus phage φ11,53 and the bacteriophage T4 long tail fiber receptorbinding tip.54 This is peculiar in cases in which a single-domain βγ-crystallin organizes as a trimer, so we investigated whether the observed trimer is a biological trimer and if there is any role of the transition metal ion in the process of trimerization. Homotrimeric Organization of Methallin and the Role of the Transition Metal Ion. With the help of small-angle Xray scattering (SAXS) experiments, we further illustrated that the trimeric arrangement observed in the crystal structure corresponds with the solution structure (Figure 3A−D). For Rg calculations, 5−23 points were used in PRIMUS43 with a qRg range of 0.476−1.29. The R g value from a Guinier approximation is 19.4 ± 0.736 Å, with an I0 value of 36.5 for 6 mg/mL protein (Figure 3A). A pair distribution curve was calculated by indirect Fourier transformation of the data, in a q range of 0.024−0.2456 Å−1, using GNOM.44 The maximal particle size (Dmax) was calculated to be 54 Å (Figure 3B). Rg and I0 values calculated from GNOM were 19.6 and 36.7 Å, respectively, which were in accordance with PRIMUS43 calculations. This pair distribution curve was used for modeling the SAXS envelope (Figure 3C). The envelope obtained by SAXS and the crystal structure trimer fits well, as the χ2 value obtained by CRYSOL46 is 0.99, indicating a good fit of both structures (Figure 3D). Furthermore, trimerization in Methallin is unusual in the sense that it is caused by ion binding. This E


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Biochemistry

Figure 4. Methallin is a high-affinity transition metal-binding βγ-crystallin. (A) Bar graph showing the Fe and Ni concentrations in the purified Methallin as measured using atomic absorption spectroscopy. (B−F) High-affinity metal binding in solution demonstrated by ITC. Thermograms showing the titration data and integrated heat measurements at 30 °C for the interaction of (B) Fe2+ and (C) Ni2+ and at 55 °C for the interaction of (D) Ni2+, (E) Co2+, and (F) Zn2+ with Methallin. Data were fit to one set of sites. The best fit values of thermodynamic parameters are listed in Table 2.

remains structurally intact (Figure 4D and Table 2). We further found that Methallin also binds Co2+ and Zn2+ with comparable affinities at this temperature (Figure 4E,F and Table 2). On the basis of comparable affinities for different transition metal ions, it could be suggested that any of these metal ions can act as the biological ligand depending on their bioavailability.57,58 Furthermore, M. thermophila is an anaerobe, and aerobic and anaerobic conditions can also influence metal ion binding.57 Methallin Is a Naturally Occurring Trimer for HighAffinity Transition Metal Ion Binding. As the trimeric state displayed by a βγ-crystallin was highly unanticipated, we further checked if the mode of metal binding and trimerization observed in Methallin is a happenstance attributed to the presence of two His residues or is a natural feature of the protein. We introduced two histidine residues at structurally identical positions in a homologous bacterial βγ-crystallin, “Clostrillin” from Clostridium beijerinckii, which has a sequence identity of ∼18% and an RMSD of 2.2 Å over 76 Cα atoms when compared to Methallin. The affinity of the Clostrillin

corresponds to a stoichiometry of 3:1, whereas Ni was not detected in the sample. As M. thermophila is an obligate anaerobe, we performed isothermal titration calorimetry (ITC) experiments with Fe2+ (by including sodium dithionate). Methallin binds Fe2+ with a high (10.84 nM) affinity (Figure 4B and Table 2). The data were fit best to one set of sites with an n (number of binding sites) of ∼0.3 (0.27) implying that three molecules of the protein form one binding site. We also attempted ITC binding experiments with Fe3+, but they were unsuccessful under the conditions used [50 mM MOPS and 50 mM KCl (pH 7.0)]. Methallin also binds other transition metal ions in a similar way, such as nickel and others, with a high affinity [dissociation constant (Kd) of 44.8 nM and an n value of 0.27 at 30 °C] (Figure 4C and Table 2). As the temperature for the optimal growth of M. thermophila is 55 °C,56 nickel ion binding ITC experiments were also performed at 55 °C. The binding affinity for nickel at 55 °C was 43.5 nM, which is close to the affinity obtained at 30 °C, suggesting the suitability of this protein for strong binding at such temperatures while it F


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Biochemistry Table 2. Thermodynamic Parameters of Ion Binding Calculated via ITC Experiments Ka (M−1)

model

Kd

ΔH (cal/mol)

ΔS (cal mol−1 deg−1)

Methallin Fe2+ (at 30 °C) 2+

Ni

(at 30 °C)

Ni2+ (at 55 °C) Co2+ (at 55 °C) Zn2+ (at 55 °C)

Ni2+ (with apoprotein) Ca2+ (with Ni2+-saturated protein) Ni2+ (with Ca2+-saturated protein)

one set of sites, n = 0.27 one set of sites, n = 0.27 one set of sites, n = 0.25 one set of sites, n = 0.27 one set of sites, n = 0.27 one set of sites, n = 0.96 two sequential binding sites one set of sites, n = 0.86

(9.22 ± 5.18) × 107

10.84 nM

−3.138 × 104 ± 211.1

−67.1

6

2.23 × 10 ± 4.12 × 10

44.84 nM

−3.517 × 10 ± 259.5

−82.4

2.30 × 107 ± 7.77 × 106

43.47 nM

−7.037 × 104 ± 979.3

−181.0

(7.71 ± 3.02) × 107

12.97 nM

−7.217 × 104 ± 612.7

−184.0

2.12 × 107 ± 9.78 × 106

47.17 nM

−6.092 × 104 ± 1107

−152.0

Clostrillin S17H/S19H 1.14 × 105 ± 8.33 × 103 8.8 μM

−12.9 × 103 ± 185.2

−20.1

1.44 × 105 ± 1.6 × 103, 1.01 × 104 ± 1.1 × 103 1.85 × 105 ± 2.55 × 104

(−12.4 ± 0.17) × 103, (−1.9 ± 0.19) × 103 (−11.5 ± 0.26) × 103

−18.1, 11.7

7

6.9 μM 5.4 μM

4

−14.7

nickel, only a small fraction of protein goes to the dimeric population. Thus, it is evident that for trimerization, metal chelation via histidine residues is essential but not sufficient in the absence of a compatible interface. Therefore, the observed trimeric behavior of Methallin is a natural feature.

S17H/S19H mutant for nickel was calculated using ITC (wildtype Clostrillin does not bind nickel). ITC thermograms showed significant heat change upon nickel binding, which is not influenced much by the presence of Ca2+, but the affinity is approximately 120-fold lower (5.4 μM) than that of Methallin (44.8 nM) (Figure 5A and Table 2). The n value being close to 1 indicates that the mode of interaction is possibly different from that of Methallin. With the help of a high-resolution crystal structure (2.1 Å resolution), we could show that Clostrillin S17H/S19H binds nickel utilizing both the introduced histidines (Figure 5B and Table 1). However, unlike Methallin, it does not form a trimer. Nickel coordinations in Clostrillin S17H/S19H are formed by two histidine residues along with four water molecules (Figure 5B and Table 1), whereas in Methallin, the coordination involves six histidine residues from three Methallin molecules. The interface analysis for Methallin using the PISA server provided a ΔG value of −6.1 kcal/mol and a buried surface area of 8.7% for the interface between two protomers (for the trimer, the buried surface area per monomer is 16.7%) with a complex formation significance score of 1.59 The trimeric interface comprises a salt bridge between Arg11 and Asp21 and hydrogen bonds between Arg11 and Asp23, Gly12 and Asp27, and Gly10 and Lys15 from two protomers. Further analysis of the Methallin trimer indicated that the interface significantly involves the interaction of Phe18 from one protomer with the hydrophobic patch created by Val3, Val38, Ile64, Phe5, and Leu40 of the adjacent protomer (Figure 6A,B). Equivalent positions in Clostrillin are occupied by Gln21, Thr6, Lys44, Asp69, Tyr8, and Pro46, respectively; these residues would cause severe clashes at the interface and would not be compatible for trimer formation (Figure 6C). Hydrophobic interface residues of Methallin are extensively variable in other homologous proteins, such as M-crystallin, Ci-βγ-crystallin, Spherulin 3a, and Protein S (Figure 6D). To probe this further, we mutated two residues of hydrophobic registry, i.e., Val38 and Leu40, to Arg, which would be incompatible for trimer formation. Analytical size exclusion chromatography showed that double mutant (V38R/L40R) Methallin remains in the monomeric state (Figure 6E). Unlike the case for the wild-type protein, the addition of excess nickel (500 μM) could not induce trimerization and most of the population remained in the monomeric state. However, in the presence of excessive

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DISCUSSION The world of βγ-crystallins remains enigmatic in terms of the functional aspects as a consequence of the enormous sequence diversity, numerous domain associations, and wide distribution. In this vein, we explored a diverse βγ-crystallin from the thermophilic methanoarchaea M. thermophila. We found that the single-domain βγ-crystallin named Methallin is a transition metal-binding, trimeric βγ-crystallin and therefore is an atypical member of this superfamily. βγ-Crystallins are known for their associative properties that have been ascribed to diverse functions ranging from spore coat formation to providing transparency to the eye lens.1,4−6 Many βγ-crystallin domains are shown to be monomers, dimers, or higher-order oligomers.1,6,8,9,13 A trimeric assembly for βγ-crystallins could be seen in the crystal structure of two-domain human βB3 (PDB entry 3QK3 by Krojer et al.60) along with dimeric association typical of a βB1-crystallin;1 however, its trimeric status in solution remains to be tested. Therefore, the trimeric arrangement seen in single-domain Methallin is unprecedented. Many βγ-crystallin domains are known to bind Ca2+, and the superfamily harbors a well-designed double-clamp N/D-N/DX-X-S/T-S motif dedicated to Ca2+ binding.8,9,12,15 The novel property of transition metal ion binding manifested by a βγcrystallin domain involving hexahistidine coordination was highly unanticipated. We have shown that the engineered Clostrillin S17H/S19H mutant binds the nickel ion at the introduced histidines but does not achieve hexahistidine coordination and displays only micromolar affinity for transition metals; this clearly suggests that the mode of coordination and trimeric arrangement of Methallin are natural per se for the achievement of higher (nanomolar) affinity. Nanomolar affinity for transition metals is physiologically relevant.49,61 The mode of transition metal coordination and the ability of the protein to bind a wide array of transition metals with comparable affinities are interesting aspects that need to be explored further. However, the metal detected using G


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Biochemistry

Figure 5. Engineering a Methallin-type nickel-binding site in Clostrillin, a homologous βγ-crystallin. (A) The engineered Clostrillin S17H/S19H mutant binds nickel with a micromolar affinity (Table 2). ITC thermograms of (i) titration of the apo Clostrillin S17H/S19H mutant with Ni2+ , (ii) titration of the nickel-saturated Clostrillin S17H/S19H mutant with Ca2+, and (iii) titration of the Ca2+-saturated Clostrillin S17H/S19H mutant with Ni2+. (B) Crystal structure of the Clostrillin S17H/S19H mutant that demonstrates that nickel coordinates protein at the engineered histidine site. Unlike the case for Methallin, nickel in the Clostrillin S17H/S19H mutant is coordinated by two histidines, while the rest of the coordinations are satisfied by four water molecules. The inset shows the nickel-binding site with a 2Fo − Fc electron density map contoured at 1.5σ.

Methallin assisting the transport of the metal itself or metaldependent transport of different substrates. The presence of various novel trace metal-binding protein(s) in methanoarchaea has been suspected for a long time,58 which could be used not only as biosignatures of evolution66 but also in understanding the strategies adopted by organisms under constantly changing conditions.22,67 Despite the presence of a straight connection between trace metals and methanogenesis,68−71 not many proteins for sequestering or transporting transition metals have been identified barring a few specific metal transport systems (such as diverged Nik systems) that need further experimental validation.23,58,72 As methanogens need a large amount of iron, nickel, and other trace metals for methanogenesis,23,71 there has always been a possibility of finding novel machinery involved in matching

an atomic absorption spectrophotometer (PerkinElmer AAnalyst 700) for protein purified from E. coli grown in LB medium was iron. The affinity for a divalent metal ion for a given ligand, in general, follows the Irving−Williams series (Mg2+ < Mn2+ < Fe2+ < Co2+ < Ni2+ < Cu2+ < Zn2+).50,61,62 However, in a biological context, this trend could break to acquire the true ligand.49,63 Thus, in the context of Methallin, identification of a biological ligand would further enhance our understanding with respect to metal acquisition and transport in M. thermophila. Interestingly, the ORF upstream of Methallin is a putative ABC transporter (mthe_0036, mthe_0037). The region of residues 23−138 of Methallin is predicted to be a noncytoplasmic domain, with a signal peptide (residues 1−48) (PREDSIGNAL),64 while the localization prediction server (LOCTREE 3) predicts it to be a secreted protein with a 99% confidence score.65 Thus, there could also be a possibility of H


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Biochemistry

Figure 6. Methallin is a natural trimer. (A) Unique hydrophobic interface of Methallin that allows it to form a trimer upon metal binding at the center of the trimer. (B) Stereodiagram showing Phe18 from one protomer docking to the hydrophobic padding of another complementing protomer, which is created by a set of hydrophobic residues specific to Methallin. (C) Stereodiagram demonstrating how the residues at corresponding positions in Clostrillin S17H/S19H will have steric clashes and would therefore not permit trimer formation in Clostrillin S17H/ S19H. (D) Structure-based multiple-sequence alignment of various βγ-crystallin domains highlighting that the interface residues (cyan and black color box) in Methallin are unique to it and the corresponding registry is extensively modified in other βγ-crystallins. (E) Size exclusion chromatogram of the Methallin V38R/L40R mutant showing the protein eluting as a monomer (red). Even in the presence of 500 μM Ni2+, the major fraction remains in the monomeric form (blue). The trimeric wild-type protein is shown as a reference (in black). Molecular mass markers are highlighted with arrows: (1) carbonic anhydrase (29 kDa) and (2) ribonuclease A (13.7 kDa).

their requirements. Our finding of this high-affinity trace metalbinding protein “Methallin” strengthens these suppositions. Using molecular clock analysis, the estimated age of the M. thermophila ancestor could be >750 million years,24,73 corresponding to the Neoproterozoic era. It has been shown that during this period nickel levels would have dropped to 200 archaeal genome sequences available in public databases, only three methanoarchaea have βγ-crystallins. Currently, no apparent explanation is available for such a restricted occurrence of βγ-crystallins in archaea, particularly when genes encoding this protein are widely distributed among bacterial and eukaryotic lineages.2,14 Two methanoarchaeal βγcrystallins are quite distinct. M-Crystallin binds Ca2+ with micromolar affinity and is monomeric,12,26 whereas Methallin binds nickel, iron, and other trace metals with nanomolar affinity but does not bind Ca2+ and forms a trimer; this suggests that both methanoarchaeal ancestors could have existed in two different ecological niches. Though the particular roles of both archaeal βγ-crystallins remain to be explored in a physiological context, Methallin being from a methanogen as well as the identification of its unique features such as its nickel, iron, or other transition metal binding property and distinct trimeric state brings a new perspective to the evolutionary origins and functional roles of βγ-crystallins. The study is expected to pave the way for the discovery of new trace metal machinery and its role in methanogenesis in such methanogens.

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ASSOCIATED CONTENT

Accession Codes

The coordinates and structure factor amplitudes of Methallin and Clostrillin S17H/S19H have been deposited in the Protein Data Bank as entries 5HT7 and 5HT8, respectively.

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REFERENCES

AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. Phone: +91-40-27160222. Fax: +91-40-27160591. *E-mail: [email protected]. ORCID

Yogendra Sharma: 0000-0003-1345-8478 Author Contributions

S.S.S., R.S., and Y.S. designed the research. S.S.S. and A.A.J. performed structural analysis. S.S.S. and R.R. performed biophysical studies. M.K.J. and S.C. contributed new reagents and analytic tools. S.S.S., R.S., and Y.S. analyzed the data. S.S.S., R.S., and Y.S. wrote the paper. Funding

This work is supported by the CSIR 12th five-year network research grant (BioAge BSC0208 and BioDiscovery BSC0120) to Y.S. and J. C. Bose fellowship (SERB) to R.S. S.S.S. and A.A.J. are the recipients of CSIR fellowships. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We are grateful to Dr. Koji Mori of the National Biological Resource Centre at the National Institute of Technology and Evaluation for the kind gift of genomic DNA of M. thermophila. Dr. P. Aravind is kindly acknowledged for help in the initial J


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A Transition Metal-Binding, Trimeric Î²Î³-Crystallin from Methane

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